Nucleotide sequences and corresponding polypeptides conferring modified phenotype characteristics in plants

ABSTRACT

Methods and materials for modulating low-nitrogen tolerance levels in plants are disclosed. For example, nucleic acids encoding low nitrogen tolerance-modulating polypeptides are disclosed as well as methods for using such nucleic acids to transform plant cells. Also disclosed are plants having increased low-nitrogen tolerance levels and plant products produced from plants having increased low-nitrogen tolerance levels.

CROSS REFERENCE TO RELATED APPLICATIONS

This application in a Continuation-in-Part of application Ser. No.13/644,359 filed on Oct. 4, 2012 (pending), which is aContinuation-in-Part of application Ser. No. 13/465,846 filed on May 7,2012 (pending), and for which priority is claimed under 35 U.S.C. §120.Application Ser. No. 13/465,846 is a Division of application Ser. No.10/572,827 filed on Mar. 7, 2007 (now U.S. Pat. No. 8,193,409).Application Ser. No. 10/572,827 is a national phase under 35 U.S.C. §371of PCT International Application No. PCT/US2003/025997 which has theInternational filing date of Aug. 18, 2003, which designated the UnitedStates of America. The entire contents of each of the above-identifiedapplications are hereby incorporated by reference, including theirsequence listings.

This application in a Continuation-in-Part of application Ser. No.14/175,856 filed on Feb. 7, 2014 (pending), which is a Reissue ofapplication Ser. No. 12/281,616 filed on Dec. 5, 2008 (now U.S. Pat. No.8,110,724). Application Ser. No. 12/281,616 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2007/06651 whichhas the International filing date of Mar. 14, 2007, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 60/821,639 filed on Aug. 7,2006, and U.S. Provisional Application No. 60/782,428 filed on Mar. 14,2006 (expired). The entire contents of each of the above-identifiedapplications are hereby incorporated by reference, including theirsequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 11/779,266 filed on Jul.17, 2007 (pending) and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 11/779,266 is a Continuation-in-Part ofapplication Ser. No. 11/778,060 filed Jul. 15, 2007 (abandoned).Application Ser. No. 11/778,060 is a Continuation-in-Part of applicationSer. No. 11/248,547 filed Oct. 12, 2005 (now U.S. Pat. No. 7,244,879).The entire contents of each of which are hereby incorporated byreference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/514,991 filed on Jan. 8,2010 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/514,991 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2007/085007 whichhas the International filing date of Nov. 16, 2007, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 60/859,467 filed Nov. 16,2006 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/445,005 filed on Jul.13, 2011 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/445,005 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2007/081301 whichhas the International filing date of Oct. 12, 2007, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 60/851,585 filed Oct. 12,2006 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/515,707 filed on Dec.16, 2009 (abandoned) and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/515,707 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2007/085439 whichhas the International filing date of Nov. 21, 2007, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 60/860,296 filed Nov. 21,2006 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/615,920 filed on Nov.10, 2009 (now U.S. Pat. No. 8,471,099), and for which priority isclaimed under 35 U.S.C. §120. Application Ser. No. 12/615,920 is aContinuation of application Ser. No. 11/114,963 filed on Apr. 25, 2005(now U.S. Pat. No. 7,696,409). Application Ser. No. 11/114,963 claimspriority under 35 U.S.C. §119(e) of U.S. Provisional Application No.60/564,659 filed Apr. 23, 2004 (expired). The entire contents of each ofwhich are hereby incorporated by reference, including their sequencelistings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/605,261 filed on Oct.23, 2009 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/605,261 is a Division of application Ser.No. 11/298,391 filed on Dec. 8, 2005 (now U.S. Pat. No. 7,663,027).Application Ser. No. 11/298,391 claims priority under 35 U.S.C. §119(e)of U.S. Provisional Application Nos. 60/635,115, filed Dec. 8, 2004 and60/635,140 filed on Dec. 8, 2004 (expired). The entire contents of eachof which are hereby incorporated by reference, including their sequencelistings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/377,106 filed on Aug.13, 2010 (abandoned) and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/377,106 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2007/075747 whichhas the International filing date of Aug. 10, 2007, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 60/837,434 filed Aug. 11,2006 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/541,607 filed on Aug.14, 2009 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/541,607 is a Continuation of applicationSer. No. 11/140,347 filed on May 27, 2005 (now U.S. Pat. No. 7,576,260).Application Ser. No. 11/140,347 claims priority under 35 U.S.C. §119(e)of U.S. Provisional Application No. 60/575,309 filed May 27, 2004(expired). The entire contents of each of which are hereby incorporatedby reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 13/184,361 filed on Jul.15, 2011 (pending), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 13/184,361 is a Division of application Ser.No. 11/140,450 filed on May 27, 2005 (now U.S. Pat. No. 8,022,273).Application Ser. No. 11/140,450 claims priority under 35 U.S.C. §119(e)of U.S. Provisional Application No. 60/575,253 filed May 27, 2004(expired). The entire contents of each of which are hereby incorporatedby reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 11/654,357 filed on Jan.16, 2007 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 11/654,357 is a Non-Provisional which claimspriority under 35 U.S.C. §119(e) of U.S. Provisional Application Nos.60/778,568 filed Mar. 1, 2006 and 60/758,831 filed on Jan. 13, 2006(expired). The entire contents of each of which are hereby incorporatedby reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 13/465,841 filed on May 7,2012 (pending) and for which priority is claimed under 35 U.S.C. §120.Application Ser. No. 13/465,841 is a Division of application Ser. No.11/858,117 filed on Sep. 19, 2007 (abandoned). Application Ser. No.11/858,117 is a Continuation-in-Part of Application No. PCT/US2007/06544which has the International filing date of Mar. 14, 2007, and whichclaims priority under 35 U.S.C. §119(e) of U.S. Provisional ApplicationNo. 60/782,735 filed Mar. 14, 2006 (expired). The entire contents ofeach of which are hereby incorporated by reference, including theirsequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/918,609 filed on Nov.22, 2010 (abandoned) and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/918,309 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2009/034638 whichhas the International filing date of Feb. 20, 2009, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 61/030,152, filed Feb. 20,2008 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/922,143 filed on Feb. 1,2011 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/922,143 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2009/037025 whichhas the International filing date of Mar. 12, 2009, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 61/036,396, filed Mar. 13,2008 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 11/241,685 filed on Sep.30, 2005 (now U.S. Pat. No. 8,481,814), and for which priority isclaimed under 35 U.S.C. §120. Application Ser. No. 11/241,685 is anon-provisional which claims priority under 35 U.S.C. §119(e) of U.S.Provisional Application No. 60/615,080, filed on Sep. 30, 2004(expired). The entire contents of each of which are hereby incorporatedby reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/863,773 filed on Nov.23, 2010 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/863,773 is a national phase under 35U.S.C. §371 of PCT International Application No. PCT/US2009/031609 whichhas the International filing date of Jan. 21, 2009, which designated theUnited States of America, and which claims priority under 35 U.S.C.§119(e) of U.S. Provisional Application No. 61/022,786 filed Jan. 22,2008 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/282,342 filed on Nov.17, 2008 (now U.S. Pat. No. 8,324,454), and for which priority isclaimed under 35 U.S.C. §120. Application Ser. No. 12/282,342 is anational phase under 35 U.S.C. §371 of PCT International Application No.PCT/US2007/06544 which has the International filing date of Mar. 14,2007, which designated the United States of America, and which claimspriority under 35 U.S.C. §119(e) of U.S. Provisional Application No.60/782,735, filed Mar. 14, 2006 (expired). The entire contents of eachof which are hereby incorporated by reference, including their sequencelistings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/776,319 filed on May 7,2010 (abandoned), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/776,319 is a Division of application Ser.No. 11/324,093 filed on Dec. 29, 2005 (now U.S. Pat. No. 7,803,983).Application Ser. No. 11/324,093 is a Continuation-in-Part of applicationSer. No. 11/172,740 filed on Jun. 30, 2005 (now U.S. Pat. No.7,396,979). Application Ser. No. 11/172,740 claims priority under 35U.S.C. §119(e) of U.S. Provisional Application Nos. 60/584,829,60/583,621, and 60/584,800, all filed on Jun. 30, 2004 (expired). Theentire contents of each of which are hereby incorporated by reference,including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 12/911,698 filed on Oct.25, 2010 (pending), and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 12/911,698 is a Division of application Ser.No. 11/324,098 filed on Dec. 29, 2005 (now U.S. Pat. No. 7,884,261).Application Ser. No. 11/324,098 is a Continuation-in-Part of applicationSer. No. 11/172,740 filed on Jun. 30, 2005 (now U.S. Pat. No.7,396,979). Application Ser. No. 11/172,740 claims priority under 35U.S.C. §119(e) of U.S. Provisional Application Nos. 60/584,829,60/583,621, and 60/584,800, all filed on Jun. 30, 2004 (expired). Theentire contents of each of which are hereby incorporated by reference,including their sequence listings.

Application Ser. No. 13/644,359 filed on Oct. 4, 2012 (pending) is aContinuation-in-Part of application Ser. No. 13/609,176 filed on Sep.10, 2012 (abandoned) and for which priority is claimed under 35 U.S.C.§120. Application Ser. No. 13/609,176 is a Division of application Ser.No. 12/139,269 filed on Jun. 13, 2008 (abandoned). Application Ser. No.12/139,269 is a Division of application Ser. No. 11/172,740 filed onJun. 30, 2005 (now U.S. Pat. No. 7,396,979). Application Ser. No.11/172,740 claims priority under 35 U.S.C. §119(e) of U.S. ProvisionalApplication Nos. 60/584,829, 60/583,621, and 60/584,800, all filed onJun. 30, 2004 (expired). The entire contents of each of which are herebyincorporated by reference, including their sequence listings.

REFERENCE TO SEQUENCE LISTING SUBMITTED VIA EFS-WEB

This application is being filed electronically via EFS-Web and includesan electronically submitted sequence listing in .txt format. The .txtfile contains a sequence listing entitled “2015-05-292750_(—)2197PUS2_Sequence_Listing.txt” created on May 29, 2015, and is21,939,971 bytes in size. The sequence listing contained in this .txtfile is part of the specification and is hereby incorporated byreference herein in its entirety.

TECHNICAL FIELD

The present invention relates to methods and materials involved intolerance of a plant to limiting exogenous nitrogen sources. Forexample, this document provides plants having increased low-nitrogentolerance levels as well as materials and methods for making plants andplant products having increased low-nitrogen tolerance levels.

BACKGROUND

Nitrogen is often the rate-limiting element in plant growth, and allfield crops have a fundamental dependence on exogenous nitrogen sources.

According to a recent study published in Field Crops Research (Volume100, Issues 2-3, 1 Feb. 2007, Pages 210-217), Nitrogenous fertilizer,which is usually supplied as ammonium nitrate, potassium nitrate, orurea, typically accounts for 40% of the costs associated with crops,such as corn and wheat in intensive agriculture.

Improving nitrogen use efficiency of crop plants is an important goaltowards reducing input costs and reducing the environmental consequencesof intensive nitrogen fertilization on the environment. Increasedefficiency of nitrogen use by plants should enable the production ofhigher yields with existing fertilizer inputs and/or enable existingyields of crops to be obtained with lower fertilizer input, or betteryields on soils of poorer quality. Also, higher amounts of proteins inthe crops could also be produced more cost-effectively.

Plants have a number of means to cope with nutrient deficiencies, suchas poor nitrogen availability. One important mechanism senses nitrogenavailability in the soil and respond accordingly by modulating geneexpression while a second mechanism is to sequester or store nitrogen intimes of abundance to be used later. The nitrogen sensing mechanismrelies on regulated gene expression and enables rapid physiological andmetabolic responses to changes in the supply of inorganic nitrogen inthe soil by adjusting nitrogen uptake, reduction, partitioning,remobilization and transport in response to changing environmentalconditions. Nitrate acts as a signal to initiate a number of responsesthat serve to reprogram plant metabolism, physiology and development(Redinbaugh et al. (1991) Physiol. Plant. 82, 640-650.; Forde (2002)Annual Review of Plant Biology 53, 203-224). Nitrogen-inducible geneexpression has been characterized for a number of genes in some detail.These include nitrate reductase, nitrite reductase, 6-phosphoglucantedehydrogenase, and nitrate and ammonium transporters (Redinbaugh et al.(1991) Physiol. Plant. 82, 640-650; Huber et al. (1994) Plant Physiol106, 1667-1674; Hwang et al. (1997) Plant Physiol. 113, 853-862;Redinbaugh et al. (1998) Plant Science 134, 129-140; Gazzarrini et al.(1999) Plant Cell 11, 937-948; Glass et al. (2002) J. Exp. Bot. 53,855-864; Okamoto et al. (2003) Plant Cell Physiol. 44, 304-317).

In the fields of agriculture and forestry, efforts are constantly beingmade to produce plants with an increased growth potential in order tofeed the ever-increasing world population and to guarantee the supply ofreproducible raw materials. There is a need for methods of increasingnitrogen use efficiency in plants, which leads to better growthpotential and more biomass. This is done conventionally through plantbreeding. The breeding process is, however, both time-consuming andlabor-intensive. Furthermore, appropriate breeding programs must beperformed for each relevant plant species. In addition, although greatprogresses that have been made about nitrogen utilization and thecomponents involved in nitrogen use efficiency, such as nitrogen uptake,nitrogen assimilation and nitrogen partitioning or remobilization, muchis still unknown about many of these complex interactions. Therefore,there is a continuing need for generally applicable processes thatimprove forest or agricultural plant growth to suit particular needsdepending on specific environmental conditions. For example, genes thatconfer tolerance to growth on low nitrogen supply are valuable productprototypes for manipulating nitrogen use efficiency in plants (Good etal., 2004). One strategy to achieve such desirable traits involvesgenetic manipulation of plant characteristics through the introductionof exogenous nucleic acids conferring increased efficiency of nitrogenuse by plants, which in turn should enable the production of higheryields with existing fertilizer inputs and/or enable existing yields ofcrops to be obtained with lower fertilizer input, or better yields onsoils of poorer quality. Such approaches have the advantage of notusually being limited to one plant species, but instead beingtransferable among plant species. The present invention relates to amethod for increasing growth potential, and/or increasing levels ofnitrogen use efficiency in plants, characterized by expression ofrecombinant DNA molecules stably integrated into the plant genome

SUMMARY

The present invention provides methods and materials related to plantshaving modulated levels of low-nitrogen tolerance. For example, thepresent invention provides transgenic plants and plant cells havingincreased levels of low-nitrogen tolerance, nucleic acids (i.e. isolatedpolynucleotides), polypeptides encoded thereby used to generatetransgenic plants and plant cells having increased levels oflow-nitrogen tolerance, and methods for making plants and plant cellshaving increased levels of low-nitrogen tolerance. Such plants and plantcells can be grown under limiting exogenous nitrogen without stuntedgrowth and diminished yields. Plants having increased low-nitrogentolerance levels may be useful to produce biomass which may be convertedto a liquid fuel or other chemicals and/or to produce food and feed onland that is currently marginally productive, resulting in an overallexpansion of arable land.

Methods of producing a plant tissue are provided herein. In one aspect,a method comprises growing a plant cell comprising an exogenous nucleicacid. The exogenous nucleic acid comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide. The HiddenMarkov Model (HMM) bit score of the amino acid sequence of thepolypeptide is greater than about 20, using an HMM generated from theamino acid sequences depicted in one of FIGS. 1-57. The tissue has adifference in the level of low-nitrogen tolerance as compared to thecorresponding level in tissue of a control plant that does not comprisethe exogenous nucleic acid.

In another aspect, a method comprises growing a plant cell comprising anexogenous nucleic acid. The exogenous nucleic acid comprises aregulatory region operably linked to a nucleotide sequence encoding apolypeptide having 80 percent or greater sequence identity to an aminoacid sequence set forth in SEQ ID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186,SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ IDNO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646,SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ IDNO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982,SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ IDNO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194,SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ IDNO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463,SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ IDNO:1554, or SEQ ID NO:1577. A plant and/or plant tissues produced fromthe plant cell has a difference in the level of low-nitrogen toleranceas compared to the corresponding level of low-nitrogen tolerance of acontrol plant that does not comprise the exogenous nucleic acid.

In another aspect, a method comprises growing a plant cell comprising anexogenous nucleic acid. The exogenous nucleic acid comprises aregulatory region operably linked to a nucleotide sequence having 80percent or greater sequence identity to a nucleotide sequence, or afragment thereof, set forth in SEQ ID NO:1, SEQ ID NO:48, SEQ ID NO:76,SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175,SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ IDNO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612,SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ IDNO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975,SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ IDNO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184,SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ IDNO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462,SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ IDNO:1553, or SEQ ID NO:1576. A plant and/or plant tissues produced fromthe plant cell has a difference in the level of low-nitrogen toleranceas compared to the corresponding level low-nitrogen tolerance of acontrol plant that does not comprise the exogenous nucleic acid.

In another aspect, the invention provides a method of producing a plant,the method comprising growing a plant cell comprising an exogenousnucleic acid that is effective for downregulating an endogenous nucleicacid in the plant cell, wherein the endogenous nucleic acid encodes apolypeptide, and wherein the HMM bit score of the amino acid sequence ofthe polypeptide is greater than about 20, said HMM based on the aminoacid sequences depicted in one of FIGS. 1-57

Methods of modulating the level of low-nitrogen tolerance in a plant areprovided herein. In one aspect, a method comprises introducing into aplant cell an exogenous nucleic acid, that comprises a regulatory regionoperably linked to a nucleotide sequence encoding a polypeptide. The HMMbit score of the amino acid sequence of the polypeptide is greater thanabout 20, using an HMM generated from the amino acid sequences depictedin one of FIGS. 1-57. A plant and/or plant tissue produced from theplant cell has a difference in the level of low-nitrogen tolerance ascompared to the corresponding level of low-nitrogen tolerance of acontrol plant that does not comprise the exogenous nucleic acid.

In certain embodiments, the HMM bit score of the amino acid sequence ofthe polypeptide is greater than about 40, using an HMM generated fromthe amino acid sequences depicted in one of FIGS. 1-57, wherein thepolypeptide comprises a Pfam domain having 70 percent or greatersequence identity to a Pfam domain of any one of the polypeptides in thesequence listing.

In another aspect, a method comprises modulating the level oflow-nitrogen tolerance in a plant by introducing into a plant cell anexogenous nucleic acid that comprises a regulatory region operablylinked to a nucleotide sequence encoding a polypeptide having 80 percentor greater sequence identity to an amino acid sequence set forth in SEQID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ IDNO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368,SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ IDNO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828,SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ IDNO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099,SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ IDNO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274,SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ IDNO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510,SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, or SEQ ID NO:1577, or afragment thereof. A plant and/or plant tissue produced from the plantcell has a difference in the level of low-nitrogen tolerance as comparedto the corresponding level of low-nitrogen tolerance of a control plantthat does not comprise the exogenous nucleic acid.

In another aspect, a method comprises modulating the level oflow-nitrogen tolerance in a plant by introducing into a plant cell anexogenous nucleic acid, that comprises a regulatory region operablylinked to a nucleotide sequence having 80 percent or greater sequenceidentity to a nucleotide sequence set forth in SEQ ID NO:1, SEQ IDNO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ IDNO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367,SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ IDNO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827,SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ IDNO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098,SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ IDNO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273,SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ IDNO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524,SEQ ID NO:1536, SEQ ID NO:1553, or SEQ ID NO:1576, or a fragmentthereof. A plant and/or plant tissue produced from the plant cell has adifference in the level of low-nitrogen tolerance as compared to thecorresponding level of low-nitrogen tolerance of a control plant thatdoes not comprise the exogenous nucleic acid.

Plant cells comprising an exogenous nucleic acid are provided herein. Inone aspect, the exogenous nucleic acid comprises a regulatory regionoperably linked to a nucleotide sequence encoding a polypeptide. The HMMbit score of the amino acid sequence of the polypeptide is greater thanabout 20, using an HMM based on the amino acid sequences depicted in oneof FIGS. 1-57. The plant has a difference in the level of low-nitrogentolerance as compared to the corresponding level of low-nitrogentolerance of a control plant that does not comprise the exogenousnucleic acid. In another aspect, the exogenous nucleic acid comprises aregulatory region operably linked to a nucleotide sequence encoding apolypeptide having 80 percent or greater sequence identity to an aminoacid sequence selected from the group consisting of SEQ ID NO:3, SEQ IDNO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ IDNO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510,SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ IDNO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853,SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ IDNO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112,SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ IDNO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302,SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ IDNO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525,SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577. A plant and/or planttissue produced from the plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise theexogenous nucleic acid. In another aspect, the exogenous nucleic acidcomprises a regulatory region operably linked to a nucleotide sequencehaving 80 percent or greater sequence identity to a nucleotide sequenceselected from the group consisting of SEQ ID NO:1, SEQ ID NO:48, SEQ IDNO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ IDNO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509,SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ IDNO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852,SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ IDNO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111,SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ IDNO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301,SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ IDNO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536,SEQ ID NO:1553, and SEQ ID NO:1576, or a fragment thereof. A plantand/or plant tissue of a plant produced from the plant cell has adifference in the level of low-nitrogen tolerance as compared to thecorresponding level of low-nitrogen tolerance of a control plant thatdoes not comprise the exogenous nucleic acid. A transgenic plantcomprising such a plant cell is also provided.

Isolated nucleic acids are also provided. In one aspect, an isolatednucleic acid comprises a nucleotide sequence having 80% or greatersequence identity to the nucleotide sequence set forth in SEQ ID NO:1,SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151,SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ IDNO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557,SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ IDNO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916,SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ IDNO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158,SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ IDNO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408,SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ IDNO:1524, SEQ ID NO:1536, SEQ ID NO:1553, or SEQ ID NO:1576. In anotheraspect, an isolated nucleic acid comprises a nucleotide sequenceencoding a polypeptide having 80% or greater sequence identity to theamino acid sequence set forth in SEQ ID NO:3, SEQ ID NO:49, SEQ IDNO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ IDNO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533,SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ IDNO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855,SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ IDNO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116,SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ IDNO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342,SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ IDNO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537,SEQ ID NO:1554, or SEQ ID NO:1577.

In another aspect, methods of identifying a genetic polymorphismassociated with variation in the level of low-nitrogen tolerance areprovided. The methods include providing a population of plants, anddetermining whether one or more genetic polymorphisms in the populationare genetically linked to the locus for a polypeptide selected from thegroup consisting of the polypeptides depicted in FIGS. 1-57, SEQ IDNO:556, SEQ ID NO:853, SEQ ID NO:1157, and functional homologs thereof,such as those in the Sequence Listing. The correlation between variationin the level of low-nitrogen tolerance in a tissue in plants of thepopulation and the presence of the one or more genetic polymorphisms inplants of the population is measured, thereby permitting identificationof whether or not the one or more genetic polymorphisms are associatedwith such variation.

In another aspect, the invention provides a method of making a plantline, said method comprising:

a) determining whether one or more genetic polymorphisms in a populationof plants is associated with the locus for a polypeptide selected fromthe group consisting of the polypeptides depicted in FIGS. 1-57, SEQ IDNO: 556, SEQ ID NO: 853, and SEQ ID NO: 1157 and functional homologsthereof;

b) identifying one or more plants in said population in which thepresence of at least one allele at said one or more geneticpolymorphisms is associated with variation in a trait;

c) crossing each said one or more identified plants with itself or adifferent plant to produce seed;

d) crossing at least one progeny plant grown from said seed with itselfor a different plant; and

e) repeating steps c) and d) for an additional 0-5 generations to makesaid plant line, wherein said at least one allele is present in saidplant line.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is an alignment of Ceres SEEDLINE No. ME00919 (SEQ ID NO:3) withhomologous and/or orthologous amino acid sequences GI No. 5921925 (SEQID NO:4), CeresClone:1929222 (SEQ ID NO:6), CeresAnnot:1471370 (SEQ IDNO:10), GI No. 84380741 (SEQ ID NO:21), GI No. 5921926 (SEQ ID NO:22),GI No. 84514161 (SEQ ID NO:25), CeresClone:779234 (SEQ ID NO:27),CeresClone:1600726 (SEQ ID NO:29), GI No. 78183420 (SEQ ID NO:36),CeresClone:1877346 (SEQ ID NO:38), GI No. 125562440 (SEQ ID NO:39), GINo. 115477665 (SEQ ID NO:40), GI No. 1173624 (SEQ ID NO:46), and GI No.84468276 (SEQ ID NO:47). In all the alignment figures shown herein, adash in an aligned sequence represents a gap, i.e., a lack of an aminoacid at that position. Identical amino acids or conserved amino acidsubstitutions among aligned sequences are identified by boxes. FIG. 1and the other alignment figures provided herein were generated using theprogram MUSCLE version 3.52.

FIG. 2 is an alignment of ME01312 (SEQ ID NO:49) with homologous and/ororthologous amino acid sequences CeresClone:1869410 (SEQ ID NO:51),CeresAnnot:1540549 (SEQ ID NO:53), CeresClone:978708 (SEQ ID NO:58),CeresClone:1623097 (SEQ ID NO:60), GI No. 92873064 (SEQ ID NO:63), GINo. 37051131 (SEQ ID NO:64), GI No. 3341468 (SEQ ID NO:65),CeresClone:937560 (SEQ ID NO:67), CeresClone:456844 (SEQ ID NO:69), GINo. 125564100 (SEQ ID NO:70), GI No. 52077334 (SEQ ID NO:71), GI No.113205234 (SEQ ID NO:73), and CeresAnnot:6100272 (SEQ ID NO:75).

FIG. 3 is an alignment of ME01463 (SEQ ID NO:77) with homologous and/ororthologous amino acid sequences GI No. 2811029 (SEQ ID NO:78),CeresClone:1853284 (SEQ ID NO:80), CeresAnnot:1476446 (SEQ ID NO:82),CeresClone:527024 (SEQ ID NO:87), GI No. 27527063 (SEQ ID NO:88),CeresClone:913632 (SEQ ID NO:90), CeresClone:1386710 (SEQ ID NO:92), GINo. 115461885 (SEQ ID NO:93), and CeresAnnot:6054519 (SEQ ID NO:95)

FIG. 4 is an alignment of ME01910 (SEQ ID NO:100) with homologous and/ororthologous amino acid sequences GI No. 585238 (SEQ ID NO:101), GI No.90704789 (SEQ ID NO:102), CeresClone:1895729 (SEQ ID NO:104),CeresAnnot:1442808 (SEQ ID NO:108), CeresClone:1104700 (SEQ ID NO:113),GI No. 32966575 (SEQ ID NO:116), GI No. 4996567 (SEQ ID NO:117), GI No.62286644 (SEQ ID NO:118), GI No. 2623960 (SEQ ID NO:119), GI No. 585241(SEQ ID NO:120), GI No. 790929 (SEQ ID NO:122), CeresClone:579112 (SEQID NO:125), CeresClone:244199 (SEQ ID NO:137), CeresClone:1725848 (SEQID NO:144), GI No. 6474950 (SEQ ID NO:145), GI No. 125546057 (SEQ IDNO:146), GI No. 115455945 (SEQ ID NO:147), GI No. 2641211 (SEQ IDNO:149), and GI No. 30024108 (SEQ ID NO:150).

FIG. 5 is an alignment of ME02538 (SEQ ID NO:152) with homologous and/ororthologous amino acid sequences CeresClone:1843642 (SEQ ID NO:154),CeresAnnot:1459112 (SEQ ID NO:158), CeresClone:953633 (SEQ ID NO:162),and CeresClone:587957 (SEQ ID NO:164).

FIG. 6 is an alignment of ME02603 (SEQ ID NO:166) with homologous and/ororthologous amino acid sequences CeresClone:1857256 (SEQ ID NO:168),CeresAnnot:1442042 (SEQ ID NO:170), GI No. 89257469 (SEQ ID NO:174),CeresClone:389818 (SEQ ID NO:177), CeresClone:2019147 (SEQ ID NO:181),GI No. 125537720 (SEQ ID NO:182), GI No. 115443697 (SEQ ID NO:183), andGI No. 20340241 (SEQ ID NO:184).

FIG. 7 is an alignment of ME02613 (SEQ ID NO:186) with homologous and/ororthologous amino acid sequences CeresAnnot:1490274 (SEQ ID NO:188),CeresClone:873093 (SEQ ID NO:193), GI No. 6635384 (SEQ ID NO:194),CeresClone:663726 (SEQ ID NO:196), GI No. 92881411 (SEQ ID NO:197),CeresClone:686525 (SEQ ID NO:199), CeresClone:1524364 (SEQ ID NO:201),CeresClone:1742159 (SEQ ID NO:203), and GI No. 125543535 (SEQ IDNO:204).

FIG. 8 is an alignment of ME02801 (SEQ ID NO:208) with homologous and/ororthologous amino acid sequences CeresClone:981621 (SEQ ID NO:214) andCeresClone:564714 (SEQ ID NO:216).

FIG. 9 is an alignment of ME03123 (SEQ ID NO:218) with homologous and/ororthologous amino acid sequences CeresClone:1899168 (SEQ ID NO:220),CeresAnnot:1494669 (SEQ ID NO:222), CeresClone:1017441 (SEQ ID NO:225),CeresClone:1065937 (SEQ ID NO:227), CeresClone:1822919 (SEQ ID NO:229),GI No. 125553329 (SEQ ID NO:230), GI No. 115439053 (SEQ ID NO:231), andCeresAnnot:6040744 (SEQ ID NO:1052).

FIG. 10 is an alignment of ME04204 (SEQ ID NO:234) with homologousand/or orthologous amino acid sequences CeresAnnot:1519952 (SEQ IDNO:236), CeresClone:234768 (SEQ ID NO:241), GI No. 108707052 (SEQ IDNO:242), and GI No. 55978030 (SEQ ID NO:244).

FIG. 11 s an alignment of ME04477 (SEQ ID NO:246) with homologous and/ororthologous amino acid sequences CeresClone:1620215 (SEQ ID NO:248), GINo. 38016527 (SEQ ID NO:249), CeresClone:1798756 (SEQ ID NO:251),CeresAnnot:1460527 (SEQ ID NO:255), GI No. 119720772 (SEQ ID NO:260),CeresClone:708446 (SEQ ID NO:262), GI No. 92896423 (SEQ ID NO:265), GINo. 113196593 (SEQ ID NO:267), GI No. 75133829 (SEQ ID NO:268),CeresClone:1030374 (SEQ ID NO:270), CeresClone:1387149 (SEQ ID NO:274),GI No. 5031281 (SEQ ID NO:277), CeresClone:1775820 (SEQ ID NO:279), GINo. 35187687 (SEQ ID NO:286), GI No. 115468934 (SEQ ID NO:290), GI No.118424243 (SEQ ID NO:296), and CeresAnnot:6063957 (SEQ ID NO:298).

FIG. 12 is an alignment of ME04507 (SEQ ID NO:300) with homologousand/or orthologous amino acid sequences CeresAnnot:1513514 (SEQ IDNO:302), CeresClone:923483 (SEQ ID NO:310), CeresClone:304357 (SEQ IDNO:312), CeresClone:1902716 (SEQ ID NO:316), GI No. 116309713 (SEQ IDNO:319), GI No. 38345408 (SEQ ID NO:321), and CeresAnnot:6017635 (SEQ IDNO:325).

FIG. 13 is an alignment of ME04587 (SEQ ID NO:332) with homologousand/or orthologous amino acid sequences Ceres ANNOT ID no. 1474882 (SEQID NO:334), Ceres ANNOT ID no. 553243 (SEQ ID NO:338), Public GI ID no.5514645 (SEQ ID NO:339), Ceres CLONE ID no. 464376 (SEQ ID NO:341),Public GI ID no. 1345643 (SEQ ID NO:346), Public GI ID no. 5832707 (SEQID NO:347), Public GI ID no. 81157968 (SEQ ID NO:348), Public GI ID no.6118407 (SEQ ID NO:349), Public GI ID no. 5081817 (SEQ ID NO:351),Public GI ID no. 125556057 (SEQ ID NO:353), Public GI ID no. 115468946(SEQ ID NO:354), Public GI ID no. 5915860 (SEQ ID NO:356), Public GI IDno. 6979544 (SEQ ID NO:358), Public GI ID no. 5832709 (SEQ ID NO:359),Public GI ID no. 6979542 (SEQ ID NO:360), Public GI ID no. 14278923 (SEQID NO:364), Public GI ID no. 81157970 (SEQ ID NO:365), Public GI ID no.81157972 (SEQ ID NO:366), Public GI ID no. 169793907 (SEQ ID NO:2541),Public GI ID no. 84514153 (SEQ ID NO:2543), Public GI ID no. 184202209(SEQ ID NO:2544), Ceres ANNOT ID no. 8459850 (SEQ ID NO:2546), CeresANNOT ID no. 8743452 (SEQ ID NO:2548), Public GI ID no. 157327290 (SEQID NO:2549), Public GI ID no. 148839039 (SEQ ID NO:2550), Public GI IDno. 197209782 (SEQ ID NO:2551), Public GI ID no. 171906244 (SEQ IDNO:2553).

FIG. 14 is an alignment of ME04753 (SEQ ID NO:368) with homologousand/or orthologous amino acid sequences GI No. 21388658 (SEQ ID NO:369),GI No. 4704605 (SEQ ID NO:371), GI No. 90704785 (SEQ ID NO:372), GI No.115529229 (SEQ ID NO:373), GI No. 20152613 (SEQ ID NO:374),CeresClone:1916226 (SEQ ID NO:376), CeresAnnot:1460836 (SEQ ID NO:392),GI No. 83032218 (SEQ ID NO:420), GI No. 1346180 (SEQ ID NO:422),CeresClone:621487 (SEQ ID NO:425), GI No. 6273331 (SEQ ID NO:433), GINo. 92874469 (SEQ ID NO:434), GI No. 1778374 (SEQ ID NO:436), GI No.18076086 (SEQ ID NO:437), GI No. 2674201 (SEQ ID NO:438), GI No. 2267567(SEQ ID NO:440), GI No. 544426 (SEQ ID NO:441), GI No. 6911144 (SEQ IDNO:444), GI No. 469071 (SEQ ID NO:447), GI No. 1934994 (SEQ ID NO:450),GI No. 82623423 (SEQ ID NO:451), GI No. 90265701 (SEQ ID NO:454), GI No.544423 (SEQ ID NO:455), CeresClone:1320097 (SEQ ID NO:458),CeresClone:1469740 (SEQ ID NO:465), CeresClone:1740834 (SEQ ID NO:473),GI No. 2226370 (SEQ ID NO:474), GI No. 27527723 (SEQ ID NO:475),CeresClone:1762613 (SEQ ID NO:477), GI No. 125545195 (SEQ ID NO:488), GINo. 108710322 (SEQ ID NO:494), GI No. 34851124 (SEQ ID NO:504), GI No.111162637 (SEQ ID NO:505), GI No. 7024451 (SEQ ID NO:506), and GI No.1229138 (SEQ ID NO:507).

FIG. 15 is an alignment of ME04772 (SEQ ID NO:510) with homologousand/or orthologous amino acid sequences GI No. 38016521 (SEQ ID NO:511),CeresClone:1895044 (SEQ ID NO:513), CeresAnnot:1512198 (SEQ ID NO:517),CeresClone:682503 (SEQ ID NO:521), CeresClone:685324 (SEQ ID NO:523),CeresClone:1384414 (SEQ ID NO:525), CeresClone:1739919 (SEQ ID NO:527),CeresClone:2002832 (SEQ ID NO:529), GI No. 125531563 (SEQ ID NO:530),and GI No. 115478344 (SEQ ID NO:531).

FIG. 16 is an alignment of ME04909 (SEQ ID NO:533) with homologousand/or orthologous amino acid sequences CeresClone:1839156 (SEQ IDNO:535), GI No. 56605378 (SEQ ID NO:536), CeresAnnot:1467946 (SEQ IDNO:538), GI No. 110931704 (SEQ ID NO:539), GI No. 92869601 (SEQ IDNO:542), GI No. 12005328 (SEQ ID NO:543), GI No. 119331596 (SEQ IDNO:546), GI No. 7705206 (SEQ ID NO:547), GI No. 18874263 (SEQ IDNO:548), CeresClone:753605 (SEQ ID NO:550), CeresClone:291733 (SEQ IDNO:552), and GI No. 21902114 (SEQ ID NO:553).

FIG. 17 is an alignment of ME05194 (SEQ ID NO:558) with homologousand/or orthologous amino acid sequences GI No. 400972 (SEQ ID NO:559),GI No. 81158002 (SEQ ID NO:560), CeresClone:1834135 (SEQ ID NO:569),CeresAnnot:1467218 (SEQ ID NO:571), CeresClone:1104143 (SEQ ID NO:575),GI No. 87240745 (SEQ ID NO:576), GI No. 13161397 (SEQ ID NO:577), GI No.18652400 (SEQ ID NO:578), GI No. 18652398 (SEQ ID NO:579),CeresClone:778892 (SEQ ID NO:581), CeresClone:222523 (SEQ ID NO:583), GINo. 82492267 (SEQ ID NO:584), GI No. 41393750 (SEQ ID NO:585), GI No.4335857 (SEQ ID NO:586), CeresClone:1776394 (SEQ ID NO:588), GI No.125555681 (SEQ ID NO:589), GI No. 115468460 (SEQ ID NO:590), and GI No.51980210 (SEQ ID NO:591).

FIG. 18 is an alignment of ME05267 (SEQ ID NO:593) with homologousand/or orthologous amino acid sequences CeresAnnot:1511954 (SEQ IDNO:595), CeresClone:560687 (SEQ ID NO:599), CeresClone:579724 (SEQ IDNO:603), CeresClone:286197 (SEQ ID NO:605), and GI No. 115489090 (SEQ IDNO:610).

FIG. 19 is an alignment of ME05300 (SEQ ID NO:613) with homologousand/or orthologous amino acid sequences CeresAnnot:6431448 (SEQ IDNO:615), CeresClone:969084 (SEQ ID NO:620), CeresClone:471052 (SEQ IDNO:622), CeresClone:733048 (SEQ ID NO:624), CeresClone:1062332 (SEQ IDNO:626), CeresClone:1743166 (SEQ ID NO:634), CeresClone:1778589 (SEQ IDNO:638), GI No. 125548354 (SEQ ID NO:643), and GI No. 115458464 (SEQ IDNO:644).

FIG. 20 is an alignment of ME05341 (SEQ ID NO:646) with homologousand/or orthologous amino acid sequences CeresClone:1808421 (SEQ IDNO:648), CeresAnnot:1452653 (SEQ ID NO:656), CeresClone:1660955 (SEQ IDNO:660), CeresClone:1287179 (SEQ ID NO:668), CeresClone:1770929 (SEQ IDNO:676), GI No. 125542421 (SEQ ID NO:679), GI No. 115450741 (SEQ IDNO:681), and CeresAnnot:6063505 (SEQ ID NO:685).

FIG. 21 is an alignment of ME05392 (SEQ ID NO:687) with homologousand/or orthologous amino acid sequences CeresClone:1841531 (SEQ IDNO:689), CeresAnnot:1507382 (SEQ ID NO:691), CeresClone:978410 (SEQ IDNO:699), CeresClone:527314 (SEQ ID NO:703), GI No. 92893019 (SEQ IDNO:706), CeresClone:638935 (SEQ ID NO:708), CeresClone:1437744 (SEQ IDNO:712), CeresClone:1728293 (SEQ ID NO:718), GI No. 125526460 (SEQ IDNO:721), GI No. 115463325 (SEQ ID NO:724), and GI No. 40642817 (SEQ IDNO:728).

FIG. 22 is an alignment of ME05429 (SEQ ID NO:730) with homologousand/or orthologous amino acid sequences CeresAnnot:1539629 (SEQ IDNO:732), CeresClone:682471 (SEQ ID NO:735), CeresClone:729869 (SEQ IDNO:737), GI No. 115459766 (SEQ ID NO:738), and CeresAnnot:6026765 (SEQID NO:742).

FIG. 23 is an alignment of ME05493 (SEQ ID NO:746) with homologousand/or orthologous amino acid sequences CeresAnnot:1455092 (SEQ IDNO:748), GI No. 15229284 (SEQ ID NO:751), CeresClone:961796 (SEQ IDNO:753), CeresClone:706956 (SEQ ID NO:755), GI No. 87162911 (SEQ IDNO:758), CeresClone:1061446 (SEQ ID NO:760), GI No. 125540686 (SEQ IDNO:761), GI No. 115447931 (SEQ ID NO:762), GI No. 20152976 (SEQ IDNO:763), and CeresAnnot:6007280 (SEQ ID NO:765).

FIG. 24 is an alignment of ME05885 (SEQ ID NO:769) with homologousand/or orthologous amino acid sequences CeresClone:1808741 (SEQ IDNO:771), CeresAnnot:1437729 (SEQ ID NO:773), CeresClone:952789 (SEQ IDNO:777), CeresClone:724313 (SEQ ID NO:779), CeresClone:791239 (SEQ IDNO:783), CeresClone:208975 (SEQ ID NO:785), CeresClone:1727075 (SEQ IDNO:789), and GI No. 115475611 (SEQ ID NO:790).

FIG. 25 is an alignment of ME07344 (SEQ ID NO:792) with homologousand/or orthologous amino acid sequences CeresClone:1843695 (SEQ IDNO:794), GI No. 56605376 (SEQ ID NO:799), CeresAnnot:1508502 (SEQ IDNO:801), CeresClone:1239229 (SEQ ID NO:805), GI No. 92893962 (SEQ IDNO:808), CeresClone:327364 (SEQ ID NO:810), CeresClone:1820378 (SEQ IDNO:816), GI No. 125524748 (SEQ ID NO:819), and GI No. 115435036 (SEQ IDNO:821).

FIG. 26 is an alignment of ME07859 (SEQ ID NO:824) with homologous aminoacid sequence Fragment_of_Ceres ANNOT ID no. 6007357 (SEQ ID NO:826),Fragment_of_Ceres CLONE ID no. 771707 (SEQ ID NO:1708), andFragment_of_Ceres CLONE ID no. 1790436 (SEQ ID NO:1713).

FIG. 27 is an alignment of ME08464 (SEQ ID NO:828) with homologousand/or orthologous amino acid sequences CeresAnnot:1499777 (SEQ IDNO:832), GI No. 22328730 (SEQ ID NO:837), GI No. 92886131 (SEQ IDNO:839), GI No. 559921 (SEQ ID NO:840), CeresClone:910787 (SEQ IDNO:842), CeresClone:1797432 (SEQ ID NO:844), GI No. 116310135 (SEQ IDNO:845), GI No. 38345464 (SEQ ID NO:847), and GI No. 90657544 (SEQ IDNO:850).

FIG. 28 is an alignment of ME11735 (SEQ ID NO:855) with homologousand/or orthologous amino acid sequences GI No. 35187445 (SEQ ID NO:856),CeresClone:1798230 (SEQ ID NO:858), CeresAnnot:1500963 (SEQ ID NO:862),CeresClone:567542 (SEQ ID NO:868), CeresClone:702251 (SEQ ID NO:870),CeresClone:1606777 (SEQ ID NO:876), CeresClone:1789146 (SEQ ID NO:878),GI No. 116309500 (SEQ ID NO:885), and GI No. 115446281 (SEQ ID NO:886).

FIG. 29 is an alignment of ME12910 (SEQ ID NO:891) with homologousand/or orthologous amino acid sequences CeresAnnot:1466353 (SEQ IDNO:893), CeresClone:519143 (SEQ ID NO:898), GI No. 2501497 (SEQ IDNO:901), GI No. 119394507 (SEQ ID NO:904), GI No. 62857206 (SEQ IDNO:905), CeresClone:766529 (SEQ ID NO:907), GI No. 62857204 (SEQ IDNO:908), GI No. 125534279 (SEQ ID NO:911), GI No. 115485437 (SEQ IDNO:912), GI No. 23955910 (SEQ ID NO:913), and GI No. 22759895 (SEQ IDNO:915).

FIG. 30 is an alignment of ME12927 (SEQ ID NO:917) with homologousand/or orthologous amino acid sequences CeresAnnot:1503548 (SEQ IDNO:919), CeresClone:37778 (SEQ ID NO:921), CeresClone:681297 (SEQ IDNO:923), CeresClone:575835 (SEQ ID NO:925), CeresClone:1714750 (SEQ IDNO:935), CeresClone:1721907 (SEQ ID NO:937), and GI No. 115451923 (SEQID NO:940).

FIG. 31 is an alignment of ME12929 (SEQ ID NO:944) with homologousand/or orthologous amino acid sequences CeresAnnot:1447562 (SEQ IDNO:946), GI No. 98962139 (SEQ ID NO:947), CeresClone:641607 (SEQ IDNO:950), CeresClone:1715150 (SEQ ID NO:962), CeresClone:1873767 (SEQ IDNO:964), GI No. 115468306 (SEQ ID NO:967), and CeresAnnot:6059980 (SEQID NO:972).

FIG. 32 is an alignment of ME12954 (SEQ ID NO:976) with homologousand/or orthologous amino acid sequences CeresClone:957229 (SEQ IDNO:978) and CeresAnnot:1496202 (SEQ ID NO:980).

FIG. 33 is an alignment of ME12970 (SEQ ID NO:982) with homologousand/or orthologous amino acid sequences CeresClone:1935438 (SEQ IDNO:984), GI No. 117573664 (SEQ ID NO:985), GI No. 68349002 (SEQ IDNO:991), GI No. 68348998 (SEQ ID NO:992), CeresAnnot:1497170 (SEQ IDNO:995), GI No. 15221718 (SEQ ID NO:996), GI No. 3860331 (SEQ IDNO:1001), CeresClone:1075911 (SEQ ID NO:1003), GI No. 2920839 (SEQ IDNO:1008), CeresClone:698452 (SEQ ID NO:1011), CeresClone:2019456 (SEQ IDNO:1023), GI No. 90399071 (SEQ ID NO:1026), GI No. 115459588 (SEQ IDNO:1028), and GI No. 68349016 (SEQ ID NO:1032).

FIG. 34 is an alignment of ME13021 (SEQ ID NO:1054) with homologousand/or orthologous amino acid sequences GI No. 2493647 (SEQ ID NO:1055),CeresClone:1924252 (SEQ ID NO:1057), GI No. 461736 (SEQ ID NO:1058),CeresAnnot:1542060 (SEQ ID NO:1061), GI No. 15226314 (SEQ ID NO:1068),GI No. 464727 (SEQ ID NO:1072), CeresClone:480644 (SEQ ID NO:1074), GINo. 124301264 (SEQ ID NO:1075), GI No. 1710807 (SEQ ID NO:1076), GI No.110349923 (SEQ ID NO:1077), GI No. 1762130 (SEQ ID NO:1078),CeresClone:706098 (SEQ ID NO:1080), GI No. 3790441 (SEQ ID NO:1083),CeresClone:1795282 (SEQ ID NO:1085), GI No. 125546535 (SEQ ID NO:1086),GI No. 115488160 (SEQ ID NO:1088), GI No. 84468456 (SEQ ID NO:1092), GINo. 116060917 (SEQ ID NO:1095), and CeresAnnot:6039555 (SEQ ID NO:1097).

FIG. 35 is an alignment of ME13064 (SEQ ID NO:1099) with homologousand/or orthologous amino acid sequences CeresAnnot:1528508 (SEQ IDNO:1101), CeresClone:9248 (SEQ ID NO:1103), GI No. 87240560 (SEQ IDNO:1105), GI No. 19453 (SEQ ID NO:1106), CeresClone:1795329 (SEQ IDNO:1108), and GI No. 108862979 (SEQ ID NO:1109).

FIG. 36 is an alignment of ME13071 (SEQ ID NO:1112) with homologousand/or orthologous amino acid sequences GI No. 125541485 (SEQ IDNO:1113), and GI No. 115449245 (SEQ ID NO:1114).

FIG. 37 is an alignment of ME13087 (SEQ ID NO:1116) with homologousand/or orthologous amino acid sequences CeresClone:100062822 (SEQ IDNO:1118), CeresAnnot:1440025 (SEQ ID NO:1120), GI No. 15238538 (SEQ IDNO:1123), GI No. 69111473 (SEQ ID NO:1129), GI No. 92873711 (SEQ IDNO:1132), GI No. 55734106 (SEQ ID NO:1133), GI No. 2346974 (SEQ IDNO:1134), CeresClone:569852 (SEQ ID NO:1136), CeresClone:1715326 (SEQ IDNO:1138), CeresClone:1608104 (SEQ ID NO:1140), GI No. 115456237 (SEQ IDNO:1141), GI No. 68655289 (SEQ ID NO:1143), GI No. 81022807 (SEQ IDNO:1144), GI No. 75706704 (SEQ ID NO:1145), and CeresAnnot:6016055 (SEQID NO:1147).

FIG. 38 is an alignment of ME13107 (SEQ ID NO:1159) with homologousand/or orthologous amino acid sequences CeresClone:1371824 (SEQ IDNO:1161), GI No. 22585 (SEQ ID NO:1162), GI No. 22208482 (SEQ IDNO:1163), and GI No. 16073 (SEQ ID NO:1164).

FIG. 39 is an alignment of ME13108 (SEQ ID NO:1166) with homologousand/or orthologous amino acid sequences GI No. 99109436 (SEQ IDNO:1167), CeresClone:1627939 (SEQ ID NO:1169), CeresClone:1840433 (SEQID NO:1171), CeresAnnot:1524198 (SEQ ID NO:1173), CeresClone:1650 (SEQID NO:1175), CeresClone:691979 (SEQ ID NO:1177), GI No. 92876897 (SEQ IDNO:1180), CeresClone:1774130 (SEQ ID NO:1182), and GI No. 115450018 (SEQID NO:1183).

FIG. 40 is an alignment of ME13110 (SEQ ID NO:1185) with homologousand/or orthologous amino acid sequences CeresClone:737317 (SEQ IDNO:1187), CeresClone:1880853 (SEQ ID NO:1189), GI No. 125558381 (SEQ IDNO:1190), and GI No. 115472157 (SEQ ID NO:1191).

FIG. 41 is an alignment of ME13125 (SEQ ID NO:1194) with homologousand/or orthologous amino acid sequences CeresClone:1938817 (SEQ IDNO:1196), CeresAnnot:1457245 (SEQ ID NO:1200), CeresClone:577910 (SEQ IDNO:1202), Public PUBLICCLONE ID no. 100736184 (SEQ ID NO:1203), GI No.125553355 (SEQ ID NO:1204), and GI No. 5091600 (SEQ ID NO:1205).

FIG. 42 is an alignment of ME13149 (SEQ ID NO:1210) with homologousand/or orthologous amino acid sequences GI No. 1703374 (SEQ ID NO:1211),CeresClone:1846330 (SEQ ID NO:1213), GI No. 29124979 (SEQ ID NO:1216),CeresAnnot:1531725 (SEQ ID NO:1218), GI No. 3334321 (SEQ ID NO:1229),CeresClone:571410 (SEQ ID NO:1232), GI No. 39653273 (SEQ ID NO:1233), GINo. 92875403 (SEQ ID NO:1234), GI No. 11131026 (SEQ ID NO:1235), GI No.77812440 (SEQ ID NO:1236), GI No. 89475524 (SEQ ID NO:1238), GI No.3182919 (SEQ ID NO:1239), GI No. 7643794 (SEQ ID NO:1240), GI No.1710851 (SEQ ID NO:1241), GI No. 115501471 (SEQ ID NO:1242), GI No.77999251 (SEQ ID NO:1243), GI No. 3450893 (SEQ ID NO:1249),CeresClone:704589 (SEQ ID NO:1251), CeresClone:1384151 (SEQ ID NO:1253),CeresClone:1713894 (SEQ ID NO:1259), GI No. 125560752 (SEQ ID NO:1264),GI No. 115475543 (SEQ ID NO:1265), GI No. 3182922 (SEQ ID NO:1267), GINo. 145353078 (SEQ ID NO:1268), GI No. 11131023 (SEQ ID NO:1269), GI No.47026845 (SEQ ID NO:1270), and GI No. 38353642 (SEQ ID NO:1272).

FIG. 43 is an alignment of ME13151 (SEQ ID NO:1274) with homologousand/or orthologous amino acid sequences CeresClone:1884601 (SEQ IDNO:1276), CeresAnnot:1445717 (SEQ ID NO:1280), CeresClone:527903 (SEQ IDNO:1284), GI No. 92891722 (SEQ ID NO:1285), CeresClone:790881 (SEQ IDNO:1287), CeresClone:299417 (SEQ ID NO:1289), CeresClone:1993894 (SEQ IDNO:1291), GI No. 125539547 (SEQ ID NO:1294), GI No. 48716424 (SEQ IDNO:1295), GI No. 84468278 (SEQ ID NO:1297), and CeresAnnot:6036303 (SEQID NO:1300).

FIG. 44 is an alignment of ME13153 (SEQ ID NO:1302) with homologousand/or orthologous amino acid sequences GI No. 70609690 (SEQ IDNO:1303), CeresClone:1927524 (SEQ ID NO:1305), CeresAnnot:1467310 (SEQID NO:1311), GI No. 45935270 (SEQ ID NO:1313), CeresClone:718446 (SEQ IDNO:1317), GI No. 92875133 (SEQ ID NO:1318), GI No. 1706318 (SEQ IDNO:1319), GI No. 3252856 (SEQ ID NO:1320), GI No. 1169238 (SEQ IDNO:1326), GI No. 31296711 (SEQ ID NO:1327), CeresClone:1468893 (SEQ IDNO:1330), GI No. 51587340 (SEQ ID NO:1331), CeresClone:1796201 (SEQ IDNO:1333), GI No. 125543034 (SEQ ID NO:1334), GI No. 115476804 (SEQ IDNO:1336), GI No. 75268060 (SEQ ID NO:1339), and GI No. 75268007 (SEQ IDNO:1340).

FIG. 45 is an alignment of ME13177 (SEQ ID NO:1342) with homologousand/or orthologous amino acid sequences CeresAnnot:1443786 (SEQ IDNO:1346), GI No. 15239172 (SEQ ID NO:1355), GI No. 562190 (SEQ IDNO:1363), GI No. 83032266 (SEQ ID NO:1364), CeresClone:602910 (SEQ IDNO:1366), GI No. 7242793 (SEQ ID NO:1370), GI No. 116167 (SEQ IDNO:1371), GI No. 2190259 (SEQ ID NO:1372), GI No. 5420278 (SEQ IDNO:1373), GI No. 1064931 (SEQ ID NO:1374), GI No. 6093215 (SEQ IDNO:1377), GI No. 461726 (SEQ ID NO:1378), GI No. 89111295 (SEQ IDNO:1379), GI No. 82949283 (SEQ ID NO:1380), GI No. 125537180 (SEQ IDNO:1381), GI No. 115489300 (SEQ ID NO:1382), and GI No. 55978000 (SEQ IDNO:1383).

FIG. 46 is an alignment of ME13200 (SEQ ID NO:1385) with homologousand/or orthologous amino acid sequences CeresAnnot:1503394 (SEQ IDNO:1387), GI No. 4914437 (SEQ ID NO:1390), CeresClone:638126 (SEQ IDNO:1393), GI No. 124360540 (SEQ ID NO:1394), GI No. 7981380 (SEQ IDNO:1395), GI No. 118137433 (SEQ ID NO:1396), CeresClone:1723374 (SEQ IDNO:1398), CeresClone:1785379 (SEQ ID NO:1400), GI No. 125553354 (SEQ IDNO:1401), GI No. 115471859 (SEQ ID NO:1404), and CeresAnnot:6040771 (SEQID NO:1407).

FIG. 47 is an alignment of ME13204 (SEQ ID NO:1409) with homologousand/or orthologous amino acid sequences CeresClone:1939206 (SEQ IDNO:1413), CeresAnnot:1453316 (SEQ ID NO:1415), GI No. 79319075 (SEQ IDNO:1418), GI No. 124359953 (SEQ ID NO:1419), CeresClone:891431 (SEQ IDNO:1421), GI No. 125536578 (SEQ ID NO:1424), and GI No. 20270065 (SEQ IDNO:1425).

FIG. 48 is an alignment of ME14649 (SEQ ID NO:1428) with homologousand/or orthologous amino acid sequences CeresClone:1978733 (SEQ IDNO:1430), CeresAnnot:1476165 (SEQ ID NO:1432), CeresClone:871529 (SEQ IDNO:1436), CeresClone:1043344 (SEQ ID NO:1439), CeresClone:786542 (SEQ IDNO:1442), CeresClone:346115 (SEQ ID NO:1444), CeresClone:1821683 (SEQ IDNO:1452), GI No. 125533171 (SEQ ID NO:1453), and GI No. 77553492 (SEQ IDNO:1457)

FIG. 49 is an alignment of ME16546 (SEQ ID NO:1463) with homologousand/or orthologous amino acid sequences CeresAnnot:1444102 (SEQ IDNO:1465), CeresClone:582439 (SEQ ID NO:1471), CeresClone:579953 (SEQ IDNO:1473), GI No. 125539335 (SEQ ID NO:1474), and GI No. 115445987 (SEQID NO:1476).

FIG. 50 is an alignment of ME17567 (SEQ ID NO:1491) with homologousand/or orthologous amino acid sequences CeresClone:1895876 (SEQ IDNO:1493), CeresAnnot:1464522 (SEQ ID NO:1495), CeresClone:968434 (SEQ IDNO:1499), CeresClone:686479 (SEQ ID NO:1501), CeresClone:1564962 (SEQ IDNO:1503), GI No. 125549699 (SEQ ID NO:1504), GI No. 125591612 (SEQ IDNO:1505), and CeresAnnot:6006969 (SEQ ID NO:1508).

FIG. 51 is an alignment of ME17932 (SEQ ID NO:1510) with homologousand/or orthologous amino acid sequences CeresClone:1842178 (SEQ IDNO:1512), CeresAnnot:1475265 (SEQ ID NO:1516) and CeresClone:1044646(SEQ ID NO:1520).

FIG. 52 is an alignment of ME17936 (SEQ ID NO:1525) with homologousand/or orthologous amino acid sequences CeresAnnot:1454324 (SEQ IDNO:1527), CeresClone:1652842 (SEQ ID NO:1534), and GI No. 75214620 (SEQID NO:1535).

FIG. 53 is an alignment of ME18275 (SEQ ID NO:1537) with homologousand/or orthologous amino acid sequences CeresAnnot:1514086 (SEQ IDNO:1539), CeresClone:1087909 (SEQ ID NO:1543), CeresClone:1359070 (SEQID NO:1545), GI No. 92880913 (SEQ ID NO:1548), CeresClone:932449 (SEQ IDNO:1550), and CeresClone:1788695 (SEQ ID NO:1552).

FIG. 54 is an alignment of ME18924 (SEQ ID NO:1554) with homologousand/or orthologous amino acid sequences GI No. 82469976 (SEQ IDNO:1555), CeresAnnot:1533704 (SEQ ID NO:1563), CeresClone:524404 (SEQ IDNO:1565), CeresClone:846541 (SEQ ID NO:1567), CeresClone:1769321 (SEQ IDNO:1571), GI No. 125528559 (SEQ ID NO:1572), GI No. 125572823 (SEQ IDNO:1574), and GI No. 84453208 (SEQ ID NO:1575).

FIG. 55 is an alignment of ME19182 (SEQ ID NO:1577) with homologousand/or orthologous amino acid sequences GI No. 4033417 (SEQ ID NO:1040),GI No. 5669924 (SEQ ID NO:1041), GI No. 40642617 (SEQ ID NO:1440), GINo. 90399018 (SEQ ID NO:1485), GI No. 115464117 (SEQ ID NO:1487), GI No.75164812 (SEQ ID NO:1578), CeresClone:1794223 (SEQ ID NO:1580),CeresAnnot:1471422 (SEQ ID NO:1590), CeresClone:968096 (SEQ ID NO:1607),GI No. 6752884 (SEQ ID NO:1608), GI No. 47775656 (SEQ ID NO:1609),CeresClone:1020799 (SEQ ID NO:1611), GI No. 87240865 (SEQ ID NO:1622),GI No. 2500047 (SEQ ID NO:1623), CeresClone:705340 (SEQ ID NO:1627),CeresClone:1430456 (SEQ ID NO:1637), GI No. 84619270 (SEQ ID NO:1648),and CeresClone:1821143 (SEQ ID NO:1651).

FIG. 56 is an alignment of ME20628 (SEQ ID NO:1437) with homologousand/or orthologous amino acid sequences GI No. 113367236 (SEQ IDNO:173), GI No. 115477615 (SEQ ID NO:212), GI No. 125542223 (SEQ IDNO:361), GI No. 1838976 (SEQ ID NO:421), CeresClone:1547185 (SEQ IDNO:443), CeresAnnot:1450452 (SEQ ID NO:740), and GI No. 92870675 (SEQ IDNO:1461).

FIG. 57 is an alignment of ME01821 (SEQ ID NO:97) with homologous and/ororthologous amino acid sequences Public GI ID no. 167480754 (SEQ IDNO:2013) and Public GI ID no. 83830869 (SEQ ID NO:2015).

DETAILED DESCRIPTION

The invention provides methods and materials related to modulatinglow-nitrogen tolerance levels in plants. In some embodiments, the plantsmay also have modulated levels of low-nitrogen tolerance. The methodscan include transforming a plant cell with a nucleic acid encoding a lownitrogen tolerance-modulating polypeptide, wherein expression of thepolypeptide results in a modulated level of low-nitrogen tolerance.Plant cells produced using such methods can be grown to produce plantshaving an increased tolerance to conditions with limiting exogenousnitrogen sources. Such plants can be used for the production of higheryields and biomasses with existing fertilizer inputs, and/or enableexisting yields and biomass of crops to be obtained with lowerfertilizer input, or better yields and biomasses on soils of poorerquality.

DEFINITIONS

“Amino acid” refers to one of the twenty biologically occurring aminoacids and to synthetic amino acids, including D/L optical isomers.

“Cell type-preferential promoter” or “tissue-preferential promoter”refers to a promoter that drives expression preferentially in a targetcell type or tissue, respectively, but may also lead to sometranscription in other cell types or tissues as well.

“Control plant” refers to a plant that does not contain the exogenousnucleic acid present in a transgenic plant of interest, but otherwisehas the same or similar genetic background as such a transgenic plant. Asuitable control plant can be a non-transgenic wild type plant, anon-transgenic segregant from a transformation experiment, or atransgenic plant that contains an exogenous nucleic acid other than theexogenous nucleic acid of interest.

“Domains” are groups of substantially contiguous amino acids in apolypeptide that can be used to characterize protein families and/orparts of proteins. Such domains have a “fingerprint” or “signature” thatcan comprise conserved primary sequence, secondary structure, and/orthree-dimensional conformation. Generally, domains are correlated withspecific in vitro and/or in vivo activities. A domain can have a lengthof from 10 amino acids to 400 amino acids, e.g., 10 to 50 amino acids,or 25 to 100 amino acids, or 35 to 65 amino acids, or 35 to 55 aminoacids, or 45 to 60 amino acids, or 200 to 300 amino acids, or 300 to 400amino acids.

“Down-regulation” refers to regulation that decreases production ofexpression products (mRNA, polypeptide, or both) relative to basal ornative states.

“Exogenous” with respect to a nucleic acid indicates that the nucleicacid is part of a recombinant nucleic acid construct, or is not in itsnatural environment. For example, an exogenous nucleic acid can be asequence from one species introduced into another species, i.e., aheterologous nucleic acid. Typically, such an exogenous nucleic acid isintroduced into the other species via a recombinant nucleic acidconstruct. An exogenous nucleic acid can also be a sequence that isnative to an organism and that has been reintroduced into cells of thatorganism. An exogenous nucleic acid that includes a native sequence canoften be distinguished from the naturally occurring sequence by thepresence of non-natural sequences linked to the exogenous nucleic acid,e.g., non-native regulatory sequences flanking a native sequence in arecombinant nucleic acid construct. In addition, stably transformedexogenous nucleic acids typically are integrated at positions other thanthe position where the native sequence is found. It will be appreciatedthat an exogenous nucleic acid may have been introduced into aprogenitor and not into the cell under consideration. For example, atransgenic plant containing an exogenous nucleic acid can be the progenyof a cross between a stably transformed plant and a non-transgenicplant. Such progeny are considered to contain the exogenous nucleicacid.

“Expression” refers to the process of converting genetic information ofa polynucleotide into RNA through transcription, which is catalyzed byan enzyme, RNA polymerase, and into protein, through translation of mRNAon ribosomes.

“Heterologous polypeptide” as used herein refers to a polypeptide thatis not a naturally occurring polypeptide in a plant cell, e.g., atransgenic Panicum virgatum plant transformed with and expressing thecoding sequence for a nitrogen transporter polypeptide from a Zea maysplant.

“Isolated nucleic acid” as used herein includes a naturally-occurringnucleic acid, provided one or both of the sequences immediately flankingthat nucleic acid in its naturally-occurring genome is removed orabsent. Thus, an isolated nucleic acid includes, without limitation, anucleic acid that exists as a purified molecule or a nucleic acidmolecule that is incorporated into a vector or a virus. A nucleic acidexisting among hundreds to millions of other nucleic acids within, forexample, cDNA libraries, genomic libraries, or gel slices containing agenomic DNA restriction digest, is not to be considered an isolatednucleic acid.

“Low Nitrogen Conditions” as used herein refers to nitrogenconcentrations which lead to nitrogen deficiency symptoms such as palegreen leaf color, chlorosis and reduced growth and vigor. Typically, lownitrogen conditions lead to a reduction of at least 20%, 25%, 30%, 35%,40%, 45%, 50%, 60%, 70%, 80% or 90% in growth and/or vigor.

“Modulation” of the level of low-nitrogen tolerance refers to the changein the level of tolerance of a plant to limiting exogenous nitrogensources that is observed as a result of expression of, or transcriptionfrom, an exogenous nucleic acid in a plant cell. The change inlow-nitrogen tolerance level is measured by changes in plant size andgreenness as well as greater photosynthesis efficiency, relative to thecorresponding level in control plants in an environment with limitingnitrogen supply.

“Nucleic acid” and “polynucleotide” are used interchangeably herein, andrefer to both RNA and DNA, including cDNA, genomic DNA, synthetic DNA,and DNA or RNA containing nucleic acid analogs. Polynucleotides can haveany three-dimensional structure. A nucleic acid can be double-strandedor single-stranded (i.e., a sense strand or an antisense strand).Non-limiting examples of polynucleotides include genes, gene fragments,exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA,siRNA, micro-RNA, ribozymes, cDNA, recombinant polynucleotides, branchedpolynucleotides, nucleic acid probes and nucleic acid primers. Apolynucleotide may contain unconventional or modified nucleotides.

“Operably linked” refers to the positioning of a regulatory region and asequence to be transcribed in a nucleic acid so that the regulatoryregion is effective for regulating transcription or translation of thesequence. For example, to operably link a coding sequence and aregulatory region, the translation initiation site of the translationalreading frame of the coding sequence is typically positioned between oneand about fifty nucleotides downstream of the regulatory region. Aregulatory region can, however, be positioned as much as about 5,000nucleotides upstream of the translation initiation site, or about 2,000nucleotides upstream of the transcription start site.

“Polypeptide” as used herein refers to a compound of two or more subunitamino acids, amino acid analogs, or other peptidomimetics, regardless ofpost-translational modification, e.g., phosphorylation or glycosylation.The subunits may be linked by peptide bonds or other bonds such as, forexample, ester or ether bonds. Full-length polypeptides, truncatedpolypeptides, point mutants, insertion mutants, splice variants,chimeric proteins, and fragments thereof are encompassed by thisdefinition.

“Progeny” includes descendants of a particular plant or plant line.Progeny of an instant plant include seeds formed on F₁, F₂, F₃, F₄, F₅,F₆ and subsequent generation plants, or seeds formed on BC₁, BC₂, BC₃,and subsequent generation plants, or seeds formed on F₁BC₁, F₁BC₂,F₁BC₃, and subsequent generation plants. The designation F₁ refers tothe progeny of a cross between two parents that are geneticallydistinct. The designations F₂, F₃, F₄, F₅ and F₆ refer to subsequentgenerations of self- or sib-pollinated progeny of an F₁ plant.

“Regulatory region” refers to a nucleic acid having nucleotide sequencesthat influence transcription or translation initiation and rate, andstability and/or mobility of a transcription or translation product.Regulatory regions include, without limitation, promoter sequences,enhancer sequences, response elements, protein recognition sites,inducible elements, protein binding sequences, 5′ and 3′ untranslatedregions (UTRs), transcriptional start sites, termination sequences,polyadenylation sequences, introns, and combinations thereof. Aregulatory region typically comprises at least a core (basal) promoter.A regulatory region also may include at least one control element, suchas an enhancer sequence, an upstream element or an upstream activationregion (UAR). For example, a suitable enhancer is a cis-regulatoryelement (-212 to -154) from the upstream region of the octopine synthase(ocs) gene. Fromm et al. (1989) The Plant Cell, 1:977-984.

“Up-regulation” refers to regulation that increases the level of anexpression product (mRNA, polypeptide, or both) relative to basal ornative states.

“Vector” refers to a replicon, such as a plasmid, phage, or cosmid, intowhich another DNA segment may be inserted so as to bring about thereplication of the inserted segment. Generally, a vector is capable ofreplication when associated with the proper control elements. The term“vector” includes cloning and expression vectors, as well as viralvectors and integrating vectors. An “expression vector” is a vector thatincludes a regulatory region.

Polypeptides

Polypeptides described herein include low nitrogen tolerance-modulatingpolypeptides. Low nitrogen tolerance-modulating polypeptides can beeffective to modulate low-nitrogen tolerance levels when expressed in aplant or plant cell. Such polypeptides typically contain at least onedomain indicative of low nitrogen tolerance-modulating polypeptides, asdescribed in more detail herein. Low nitrogen tolerance-modulatingpolypeptides typically have an HMM bit score that is greater than 20, asdescribed in more detail herein. In some embodiments, low nitrogentolerance-modulating polypeptides have greater than 80% identity to SEQID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ IDNO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368,SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ IDNO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828,SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ IDNO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099,SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ IDNO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274,SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ IDNO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510,SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, or SEQ ID NO:1577, asdescribed in more detail herein.

Domains Indicative of Low Nitrogen Tolerance-Modulating Polypeptides

A low nitrogen tolerance-modulating polypeptide can contain a P450domain, which is characteristic of polypeptides belonging to theCytochrome P450 superfamily. Cytochrome P450s are haem-thiolate proteinsinvolved in the oxidative degradation of various compounds. They areparticularly well known for their role in the degradation ofenvironmental toxins and mutagens. In plants, these proteins areimportant for the biosynthesis of several compounds such as hormones,defensive compounds and fatty acids. Sequence conservation is relativelylow within the family—there are only 3 absolutely conserved residues—buttheir general topography and structural fold are highly conserved. Theconserved core is composed of a coil termed the ‘meander’, a four-helixbundle, helices J and K, and two sets of beta-sheets. These constitutethe haem-binding loop, the proton-transfer groove and the conserved EXXRmotif in helix K. While prokaryotic P450s are soluble proteins, mosteukaryotic P450s are associated with microsomal membranes. Their generalenzymatic function is to catalyse regiospecific and stereospecificoxidation of non-activated hydrocarbons at physiological temperatures.SEQ ID NO:3 and SEQ ID NO:332 set forth the amino acid sequence ofArabidopsis clones, identified herein as ME00919 (SEQ ID NO:3) andME04587 (SEQ ID NO:332) respectively, that are predicted to encodepolypeptides containing a Cytochrome P450 domain.

A low nitrogen tolerance-modulating polypeptide can contain a zf-Dofdomain, which is conserved in several DNA-binding proteins of higherplants. Dof domain is a zinc finger DNA-binding domain that showsresemblance to the Cys2 zinc finger, although it has a longer putativeloop where an extra Cys residue is typically conserved. The motif isalso present in SEQ ID NO:49, which sets forth the amino acid sequenceof an Arabidopsis clone, identified herein as Ceres ME01312 (SEQ IDNO:49), that is predicted to encode a polypeptide containing a zf-Dofdomain.

A low nitrogen tolerance-modulating polypeptide can contain anAminotran_(—)3 domain characteristic of polypeptides belonging to theaminotransferase Class-III family. Aminotransferases share certainmechanistic features with other pyridoxalphosphate-dependent enzymes,such as the covalent binding of the pyridoxalphosphate group to a lysineresidue. Class-III aminotransferases include acetylornithineaminotransferase, which catalyzes the transfer of an amino group fromacetylornithine to alpha-ketoglutarate, yieldingN-acetyl-glutamic-5-semi-aldehyde and glutamic acid; ornithineaminotransferase, which catalyzes the transfer of an amino group fromornithine to alpha-ketoglutarate, yielding glutamic-5-semi-aldehyde andglutamic acid; omega-amino acid—pyruvate aminotransferase, whichcatalyzes transamination between a variety of omega-amino acids, mono-and diamines, and pyruvate; 4-aminobutyrate aminotransferase; GABAtransaminase, which catalyzes the transfer of an amino group from GABAto alpha-ketoglutarate, yielding succinate semialdehyde and glutamicacid; DAPA aminotransferase, a bacterial enzyme (bioA), which catalyzesan intermediate step in the biosynthesis of biotin, the transaminationof 7-keto-8-aminopelargonic acid to form 7,8-diaminopelargonic acid;2,2-dialkylglycine decarboxylase, a Burkholderia cepacia (Pseudomonascepacia) enzyme (dgdA) that catalyzes the decarboxylating amino transferof 2,2-dialkylglycine and pyruvate to dialkyl ketone, alanine and carbondioxide; glutamate-1-semialdehyde aminotransferase (GSA); Bacillussubtilis aminotransferases yhxA and yodT; Haemophilus influenzaeaminotransferase HI0949; and Caenorhabditis elegans aminotransferase. Onthe basis of sequence similarity, these various enzymes can be groupedinto subfamilies. The aminotran_(—)3 domain is also present in SEQ IDNO:77, which set forth the amino acid sequences of Arabidopsis clone,identified herein as Ceres ME01463 (SEQ ID NO:77), that is predicted toencode polypeptides containing an aminotran_(—)3 domain.

A low nitrogen tolerance-modulating polypeptide can contain a linkerhistone domain characteristic of polypeptides belonging to the linkerhistone H1 and H5 family. Linker histone H1 is an essential component ofchromatin structure. H1 links nucleosomes into higher order structures.Histone H5 performs the same function as histone H1, and replaces H1 incertain cells. The structure of GH5, the globular domain of the linkerhistone H5 fold is similar to the DNA-binding domain of the catabolitegene activator protein, CAP, thus providing a possible model for thebinding of GH5 to DNA. The domain is also present in SEQ ID NO:100,which sets forth the amino acid sequence of an Arabidopsis clone,identified herein as Ceres ME01910 (SEQ ID NO:100), that is predicted toencode a polypeptide containing a linker histone domain.

A low nitrogen tolerance-modulating polypeptide can contain a zf-C3HC4domain, which is predicted to be characteristic of proteins belonging tothe C3HC4 type zinc-finger (RING finger) protein family. The C3HC4 typezinc-finger (RING finger) is a cysteine-rich domain of approximately 40to 60 residues that coordinates two zinc ions, and is probably involvedin mediating protein-protein interactions. Members of the C3HC4 typezinc-finger (RING finger) protein family contain the loosely conservedsequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where Xis any amino acid. The domain is also present in SEQ ID NOs:166, 746,976, 1428, which set forth the amino acid sequences of Arabidopsisclones, identified herein as Ceres ME02603 (SEQ ID NO:166), ME05493 (SEQID NO:746), ME12954 (SEQ ID NO:976), ME14649 (SEQ ID NO:1428)respectively, that are predicted to encode polypeptides containing azf-C3HC4 domain.

A low nitrogen tolerance-modulating polypeptide can contain a Gal Lectindomain characteristic of a galactose binding lectin domain protein. SEQID NO:208 sets forth the amino acid sequence of an Arabidopsis clone,identified herein as Ceres ME02801 (SEQ ID NO:208), that is predicted toencode a polypeptide containing a galactose binding lectin domain.

A low nitrogen tolerance-modulating polypeptide can contain a TRP_(—)1domain characteristic of tetratricopeptide repeat (TPR) domain protein.The tetratricopeptide repeat is a structural motif present in a widerange of proteins identified in various different organisms, rangingfrom bacteria to humans. It mediates protein-protein interactions andthe assembly of multiprotein complexes. Sequence alignment of the TPRdomains reveals a consensus sequence defined by a pattern of small andlarge amino acids. Proteins containing TPRs are involved in a variety ofbiological processes, such as cell cycle regulation, transcriptionalcontrol, mitochondrial and peroxisomal protein transport, neurogenesisand protein folding. The X-ray structure of a domain containing threeTPRs from protein phosphatase 5 revealed that TPR adopts ahelixturnhelix arrangement, with adjacent TPR motifs packing in aparallel fashion, resulting in a spiral of repeating anti-parallelalpha-helices. The two helices are denoted helix A and helix B. Thepacking angle between helix A and helix B is ˜24° within a single TPRand generates a right-handed superhelical shape. Helix A interacts withhelix B and with helix A′ of the next TPR. Two protein surfaces aregenerated: the inner concave surface is contributed to mainly by residueon helices A, and the other surface presents residues from both helicesA and B.

A low nitrogen tolerance-modulating polypeptide can contain a TRP_(—)2tetratricopeptide repeat domain, which is predicted to be characteristicof scaffold-proteins in multiprotein complexes. The TPR_(—)2 domainconsists of approximately 34-amino-acid motif with a loose consensus andis present, usually as multiple tandem repeats, in proteins with manycellular functions, including mitosis, transcription, protein transport,and development. Structural analysis of the TPR-2 domain demonstratesthat it forms two α-helical regions separated by a turn, such thatapposed bulky and small side chains form a “knob and hole” structure. Ingeneral, the hydrophobic surface of this structure mediatesprotein-protein interactions between TPR- and non-TPR-containingproteins.

SEQ ID NO:234 sets forth the amino acid sequence of Arabidopsis clone,identified herein as Ceres ME04204 (SEQ ID NO:234), that is predicted toencode a polypeptide containing a TRP_(—)1 tetratricopeptide repeatdomain and a TRP_(—)2 tetratricopeptide repeat domain. SEQ ID NO:1510sets forth the amino acid sequence of Arabidopsis clone, identifiedherein as Ceres ME17932 (SEQ ID NO:1510), that is predicted to encode apolypeptide containing a TRP_(—)2 tetratricopeptide repeat domain.

A low nitrogen tolerance-modulating polypeptide can contain a zf-AN1domain characteristic of polypeptides belonging to the AN1-like Zincfinger domain protein family. The AN1-like Zinc finger domain was firstidentified as a zinc finger at the C-terminus of An1 a ubiquitin-likeprotein in Xenopus laevis. The following pattern describes the zincfinger: C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C, where X can be anyamino acid, and numbers in brackets indicate the number of residues.

A low nitrogen tolerance-modulating polypeptide can contain a zf-A20domain, which is characteristic of A20- (an inhibitor of celldeath)-like zinc fingers. In animals, A20-like zinc fingers are believedto mediate self-association in A20. These fingers also mediateIL-1-induced NF-kappa B activation. SEQ ID NO: 246 sets forth the aminoacid sequence of Arabidopsis clone, identified herein as Ceres ME04477(SEQ ID NO:246), that is predicted to encode a polypeptide containing anAN1-like Zinc finger domain and zf-A20 domain.

A low nitrogen tolerance-modulating polypeptide can contain an Aa_transdomain, or transmembrane amino acid transporter domain, which ispredicted to be characteristic of amino acid transporters and amino acidpermeases. The domain is also present in SEQ ID NO:300, which sets forththe amino acid sequence of an Arabidopsis clone, identified herein asCeres ME04507 (SEQ ID NO:300), that is predicted to encode a polypeptidecontaining an transmembrane amino acid transporter domain.

A low nitrogen tolerance-modulating polypeptide can contain an RNArecognition motif (as known as RRM_(—)1, RRM, RBD, or RNP domain), whichis characteristic of polypeptides belonging to the single strandRNA-binding protein superfamily. RRM proteins have a variety of RNAbinding preferences and functions, and include heterogeneous nuclearribonucleoproteins (hnRNPs), proteins implicated in regulation ofalternative splicing, protein components of small nuclearribonucleoproteins, and proteins that regulate RNA stability andtranslation. The RRM in heterodimeric splicing factor U2 snRNP auxiliaryfactor (U2AF) appears to have two RRM-like domains with specializedfeatures for protein recognition. The motif also appears in a few singlestranded DNA binding proteins. The typical RRM consists of fouranti-parallel beta-strands and two alpha-helices arranged in abeta-alpha-beta-beta-alpha-beta fold with side chains that stack withRNA bases. Specificity of RNA binding is determined by multiple contactswith surrounding amino acids. A third helix is present during RNAbinding in some cases. The motif is also present in SEQ ID NO:368 andSEQ ID NO:1274, which set forth the amino acid sequences of Arabidopsisclones, identified herein as Ceres ME04753 (SEQ ID NO:368) and ME13151(SEQ ID NO:1274) respectively, that are predicted to encode polypeptidescontaining an RNA recognition motif.

A low nitrogen tolerance-modulating polypeptide can contain an NTF2domain characteristic of a nuclear transport factor 2 (NTF2)polypeptide. NTF2 is a homodimer of approximately 14 kDa subunits whichstimulates efficient nuclear import of a cargo protein. NTF2 binds toboth RanGDP and FxFG repeat-containing nucleoporins. NTF2 binds toRanGDP sufficiently strongly for the complex to remain intact duringtransport through nucleopore complexes (NPCs), but the interactionbetween NTF2 and FxFG nucleoporins is much more transient, which wouldenable NTF2 to move through the NPC by hopping from one repeat toanother. NTF2 folds into a cone with a deep hydrophobic cavity, theopening of which is surrounded by several negatively charged residues.RanGDP binds to NTF2 by inserting a conserved phenylalanine residue intothe hydrophobic pocket of NTF2 and making electrostatic interactionswith the conserved negatively charged residues that surround the cavity.A structurally similar domain appears in other nuclear import proteins.SEQ ID NO:1274, which sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME13151 (SEQ ID NO:1274),that is predicted to encode a polypeptide containing a NTF2 domain.

A low nitrogen tolerance-modulating polypeptide can contain a DUF1218domain. SEQ ID NO:1274, which sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME04772 (SEQ ID NO:510),that is predicted to encode a polypeptide containing a DUF1218 domain.

A low nitrogen tolerance-modulating polypeptide can contain a Myb-likeDNA-binding domain characteristic of polypeptides belonging to a proteinfamily whose members contain the DNA binding domains from Myb proteins,as well as the SANT domain family. SEQ ID NO:533, which sets forth theamino acid sequence of an Arabidopsis clone, identified herein as CeresME04909 (SEQ ID NO:533), that is predicted to encode a polypeptidecontaining a Myb-like DNA-binding domain.

A low nitrogen tolerance-modulating polypeptide can contain aFAD_binding_(—)4 domain. This domain is predicted to be characteristicof polypeptides belonging to a family of enzymes that use FAD (flavinadenine dinucleotide) as a co-factor, most of the enzymes are similar tooxygen oxidoreductase, containing a covalently bound FAD group which isattached to a histidine via an 8-alpha-(N3-histidyl)-riboflavin linkage.

A low nitrogen tolerance-modulating polypeptide can contain a BBEdomain, which is predicted to be characteristic of a berberine bridgeand berberine bridge-like enzyme. BBE enzymes are typically involved inthe biosynthesis of numerous isoquinoline alkaloids. They catalyse thetransformation of the N-methyl group of (S)-reticuline into the C-8berberine bridge carbon of (S)-scoulerine. SEQ ID NO:558 sets forth theamino acid sequence of an Arabidopsis clone, identified herein as CeresME05194 (SEQ ID NO:558), that is predicted to encode a polypeptidecontaining an FAD_binding_(—)4 domain and a BBE domain.

A low nitrogen tolerance-modulating polypeptide can contain a prefoldin(PFD) domain characteristic of polypeptides belonging to the prefoldinsubunit family. Prefoldin (PFD) is a chaperone that typically interactswith type II chaperonins, hetero-oligomers lacking an obligateco-chaperonin that are found in eukaryotes (chaperonin-containingT-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD can typicallybind both actin and tubulin co-translationally. The chaperone can thendelivers the target protein to CCT, interacting with the chaperoninthrough the tips of the coiled coils. SEQ ID NO:593 sets forth the aminoacid sequence of an Arabidopsis clone, identified herein as CeresME05267 (SEQ ID NO:593), that is predicted to encode a polypeptidecontaining a prefoldin domain.

A low nitrogen tolerance-modulating polypeptide can contain an HR-lesiondomain characteristic of polypeptides belonging to a family of plantproteins can be associated with the hypersensitive response (HR) pathwayof defense against plant pathogens. The domain is also present in SEQ IDNO: 646, which sets forth the amino acid sequence of an Arabidopsisclone, identified herein as Ceres ME05341 (SEQ ID NO: 646), that ispredicted to encode a polypeptide containing an HR-lesion domain.

A low nitrogen tolerance-modulating polypeptide can contain a DUF538domain. SEQ ID NO:687 sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME05392 (SEQ ID NO:687),that is predicted to encode a polypeptide containing a DUF538 domain.

A low nitrogen tolerance-modulating polypeptide can contain a zincfinger C-x8-C-x5-C-x3-H type domain (zf-CCCH), which is characteristicof polypeptides belonging to the zinc finger protein superfamily.Members of zinc finger domains proteins are thought to be involved inDNA-binding, and exist as different types. Proteins containing zincfinger domains of the C-x8-C-x5-C-x3-H type include zinc finger proteinsfrom eukaryotes involved in cell cycle or growth phase-relatedregulation. It has been shown that different CCCH zinc finger proteinsinteract with the 3′ untranslated region of various mRNA. SEQ ID NO:792sets forth the amino acid sequence of an Arabidopsis clone, identifiedherein as Ceres ME07344 (SEQ ID NO:792), that is predicted to encode apolypeptide containing a zf-CCCH domain.

A low nitrogen tolerance-modulating polypeptide can contain a DUF246domain. SEQ ID NO:828 sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME08464 (SEQ ID NO:828),that is predicted to encode a polypeptide containing a DUF246 domain.

A low nitrogen tolerance-modulating polypeptide can contain a C2 domain.The C2 domain is a Ca2+-dependent membrane-targeting module found inmany cellular proteins involved in signal transduction or membranetrafficking C2 domains are unique among membrane targeting domains inthat they typically show wide range of lipid selectivity for the majorcomponents of cell membranes, including phosphatidylserine andphosphatidylcholine. SEQ ID NO:982 sets forth the amino acid sequence ofan Arabidopsis clone, identified herein as Ceres ME12970 (SEQ IDNO:982), that is predicted to encode a polypeptide containing an C2domain.

A low nitrogen tolerance-modulating polypeptide can contain a Cpn60_TCP1domain characteristic of polypeptides belonging to the TCP-1/cpn60chaperonin family. This family includes members from the HSP60 chaperonefamily and the TCP-1 (T-complex protein) family. Chaperonins, asubfamily of molecular chaperones, are typically essential for thecorrect folding and assembly of polypeptides into oligomeric structures.Chaperonins are typically found in abundance in prokaryotes,chloroplasts and mitochondria. They are typically required for normalcell growth, and are stress-induced, acting to stabilize or protectdisassembled polypeptides under heat-shock conditions. SEQ ID NO: 1054sets forth the amino acid sequence of an Arabidopsis clone, identifiedherein as Ceres ME13021 (SEQ ID NO: 1054), that is predicted to encode apolypeptide containing a Cpn60_TCP1 domain.

A low nitrogen tolerance-modulating polypeptide can contain a zf-C2H2domain characteristic of a C2H2 zinc finger domain polypeptide. Zincfinger domains are nucleic acid-binding protein structures composed of25 to 30 amino-acid residues including 2 conserved Cys and 2 conservedHis residues in a C-2-C-12-H-3-H type motif. The 12 residues separatingthe second Cys and the first His are mainly polar and basic, implicatingthis region in particular in nucleic acid binding. They have the abilityto bind to both RNA and DNA, and it has been suggested that the zincfinger may thus represent the original nucleic acid binding protein. Ithas also been suggested that a Zn-centered domain could be used in aprotein interaction, e.g. in protein kinase C. Many classes of zincfingers are characterized according to the number and positions of thehistidine and cysteine residues involved in the zinc atom coordination.In C2H2 zinc finger class, the first pair of zinc coordinating residuesare cysteines, while the second pair are histidines. The motif is alsopresent in SEQ ID NO:1116, which sets forth the amino acid sequence ofan Arabidopsis clone, identified herein as Ceres ME13087 (SEQ IDNO:1116), that is predicted to encode a polypeptide containing a zf-C2H2domain.

A low nitrogen tolerance-modulating polypeptide can contain a zeindomain characteristic of polypeptides belonging to the zein family ofseed storage proteins. SEQ ID NO:1159, which sets forth the amino acidsequence of an Arabidopsis clone, identified herein as Ceres ME13107(SEQ ID NO: 1159), that is predicted to encode a polypeptide containinga zein domain.

A low nitrogen tolerance-modulating polypeptide can contain a snf7domain characteristic of polypeptides belonging to a family ofeukaryotic proteins related to yeast SNF7. SEQ ID NO:1185 sets forth theamino acid sequence of an Arabidopsis clone, identified herein as CeresME13110 (SEQ ID NO:1185), that is predicted to encode a polypeptidecontaining a snf7 domain.

A low nitrogen tolerance-modulating polypeptide can contain an HhH-GPDdomain characteristic of polypeptides belonging to the HhH-GPD baseexcision DNA repair protein superfamily. Members of the HhH-GPD baseexcision DNA repair protein superfamily contain helix-hairpin-helix andGly/Pro rich loop followed by a conserved aspartate. This domain isfound in a diverse range of structurally related DNA repair proteins.The domain is also present in SEQ ID NO:1194 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as Ceres ME13125(SEQ ID NO:1194), that is predicted to encode a polypeptide containingan HhH-GPD domain.

A low nitrogen tolerance-modulating polypeptide can contain an Arfdomain characteristic of polypeptides belonging to the ADP-ribosylationfactor family. The small ADP ribosylation factor (Arf) GTP-bindingproteins are major regulators of vesicle biogenesis in intracellulartraffic. They are the founding members of a growing family that includesArl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar(Secretion-associated and Ras-related) proteins. Arf proteins cyclebetween inactive GDP-bound and active GTP-bound forms that bindselectively to effectors. The classical structural GDP/GTP switch ischaracterized by conformational changes at the so-called switch 1 andswitch 2 regions, which bind tightly to the gamma-phosphate of GTP butpoorly or not at all to the GDP nucleotide. Structural studies of Arf1and Arf6 have revealed that although these proteins feature the switch 1and 2 conformational changes, they depart from other small GTP-bindingproteins in that they use an additional, unique switch to propagatestructural information from one side of the protein to the other. TheGDP/GTP structural cycles of human Arf1 and Arf6 feature a uniqueconformational change that affects the beta2beta3 strands connectingswitch 1 and switch 2 (interswitch) and also the amphipathic helicalN-terminus. SEQ ID NO: 1210 sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME13149 (SEQ ID NO:1210),that is predicted to encode a polypeptide containing an Arf domain.

A low nitrogen tolerance-modulating polypeptide can contain aPyridoxal_deC domain characteristic of pyridoxal-dependent decarboxylasepolypeptide. Pyridoxal-dependent decarboxylases typically share regionsof sequence similarity, particularly in the vicinity of a conservedlysine residue, which provides the attachment site for thepyridoxal-phosphate (PLP) group. Pyridoxal phosphate is the active formof vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst,acting as a coenzyme in a multitude of reactions, includingdecarboxylation, deamination and transamination. PLP-dependent enzymes,including pyridoxal-dependent decarboxylases, are involved in thebiosynthesis of amino acids and amino acid-derived metabolites, but theyare also found in the biosynthetic pathways of amino sugars and in thesynthesis or catabolism of neurotransmitter. SEQ ID NO:1302 sets forththe amino acid sequence of an Arabidopsis clone, identified herein asCeres ME13153 (SEQ ID NO:1302), that is predicted to encode apolypeptide containing a Pyridoxal_deC domain.

A low nitrogen tolerance-modulating polypeptide can contain a Cyclin_Cdomain, which is characteristic to the C-terminal domain of polypeptidesbelonging to the Cyclin family. Cyclins are eukaryotic proteins thatplay an active role in controlling nuclear cell division cycles, andregulate cyclin dependent kinases (CDKs). Cyclins, together with the p34(cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF).There are two main groups of cyclins, G1/S cyclins, which play a role inthe control of the cell cycle at the G1/S (start) transition, and G2/Mcyclins, which play a role in the control of the cell cycle at the G2/M(mitosis) transition. G2/M cyclins accumulate steadily during G2 and areabruptly destroyed as cells exit from mitosis (at the end of theM-phase). Cyclins typically contain two domains of similar all-alphafold, of which this family corresponds with the C-terminal domain.

A low nitrogen tolerance-modulating polypeptide can contain a Cyclin_Ndomain, which defines the N-terminal domain of polypeptides belonging tothe Cyclin family. SEQ ID NO: 1342 sets forth the amino acid sequence ofan Arabidopsis clone, identified herein as Ceres ME13177 (SEQ ID NO:1342), that is predicted to encode a polypeptide containing a Cyclin_Cdomain and a Cyclin_N domain

A low nitrogen tolerance-modulating polypeptide can contain a DUF1442domain. SEQ ID NO:1463, which sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME16546 (SEQ ID NO:1463),that is predicted to encode a polypeptide containing a DUF1442 domain.

A low nitrogen tolerance-modulating polypeptide can contain an HLHdomain characteristic of polypeptides belonging to the Helix-loop-helixDNA-binding domain superfamily. Basic helix-loop-helix proteins (bHLH)are a group of eukaryotic transcription factors that can exert adeterminative influence in a variety of developmental pathways. Thesetranscription factors are characterized by a conserved bHLH domain thatmediates specific dimerization. They can facilitate the conversion ofinactive monomers to trans-activating dimers at appropriate stages ofdevelopment. Members of this superfamily can be classified into discretecategories according to dimerization, DNA binding and expressioncharacteristics. SEQ ID NO:1537 sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME18275 (SEQ ID NO:1537),that is predicted to encode a polypeptide containing an HLH domain.

A low nitrogen tolerance-modulating polypeptide can contain a CRAL_TRIOdomain characteristic of the C-terminal of retinaldehyde/retinal-bindingprotein family. In animals, retinaldehyde/retinal-binding proteins maybe functional components of the visual cycle. Cellularretinaldehyde-binding protein (CRALBP) may function as a substratecarrier protein that modulates interaction of these retinoids withvisual cycle enzymes. The multidomain protein Trio can bind the LARtransmembrane tyrosine phosphatase, contains a protein kinase domain,and has separate rac-specific and rho-specific guanine nucleotideexchange factor domains. Trio is a multifunctional protein that canintegrate and amplify signals involved in coordinating actin remodeling,which is necessary for cell migration and growth. Other members of thefamily are transfer proteins that include, guanine nucleotide exchangefactor that may function as an effector of RAC1,phosphatidylinositol/phosphatidylcholine transfer protein that isrequired for the transport of secretory proteins from the Golgi complexand alpha-tocopherol transfer protein that enhances the transfer of theligand between separate membranes.

A low nitrogen tolerance-modulating polypeptide can contain aCRAL_TRIO_N which defines the N-terminal ofretinaldehyde/retinal-binding protein family.

A low nitrogen tolerance-modulating polypeptide can contain anEMP24_GP25L domain characteristic of polypeptides belonging to theemp24/gp25L/p24 family/GOLD gene family. Members of this family areimplicated in bringing cargo forward from the ER and binding to coatproteins by their cytoplasmic domains. This domain corresponds closelyto the beta-strand rich GOLD domain. The GOLD domain is often foundcombined with lipid- or membrane-association domains. p24 proteins aremajor membrane components of COPI- and COPII-coated vesicles and areimplicated in cargo selectivity of ER to Golgi transport. Multiplemembers of the p24 family are found in all eukaryotes, from yeast tomammals. Members of the p24 family are type I membrane proteins with asignal peptide at the amino terminus, a lumenal coiled-coil(extracytosolic) domain, a single transmembrane domain with conservedamino acids, and a short cytoplasmic tail. They may be grouped into atleast three subfamilies based on primary sequence. One subfamilycomprises yeast Emp24p and mammalian p24A. Another subfamily comprisesyeast Erv25p and mammalian Tmp21, and the third subfamily comprisesmammalian gp25L proteins. SEQ ID NO:1554 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as Ceres ME18924(SEQ ID NO:1554), that is predicted to encode a polypeptide containing aCRAL_TRIO domain, a CRAL_TRIO_N domain, and a EMP24 GP25L domain.

A low nitrogen tolerance-modulating polypeptide can contain aPyrophosphatase domain, which is predicted to be characteristic of aninorganic pyrophosphatase (PPase). PPase is the enzyme responsible forthe hydrolysis of pyrophosphate (PPi) which is formed principally as theproduct of the many biosynthetic reactions that utilize ATP. PPases mayrequire the presence of divalent metal cations, with magnesiumconferring the highest activity. Among other residues, a lysine has beenpostulated to be part of or close to the active site. The sequences ofPPases share some regions of similarities, among which is a region thatcontains three conserved aspartates that are involved in the binding ofcations. SEQ ID NO:1577 sets forth the amino acid sequence of anArabidopsis clone, identified herein as Ceres ME19182 (SEQ ID NO:1577),that is predicted to encode a polypeptide containing a Pyrophosphatasedomain.

A low nitrogen tolerance-modulating polypeptide can contain a bZIP_(—)1domain characteristic of polypeptides belonging to the superfamily ofbasic ZIP transcription factors. Members of the eukaryotic bZIPtranscription factor superfamily contain a basic region mediatingsequence-specific DNA-binding followed by a leucine zipper regionrequired for dimerization. SEQ ID NO: 1437 sets forth the amino acidsequence of an Arabidopsis clone, identified herein as Ceres ME20628(SEQ ID NO: 1437), that is predicted to encode a polypeptide containinga bZIP_(—)1 domain.

B. Functional Homologs Identified by Reciprocal BLAST

In some embodiments, one or more functional homologs of a reference lownitrogen tolerance-modulating polypeptide defined by one or more of thePfam descriptions indicated above are suitable for use as low nitrogentolerance-modulating polypeptides. A functional homolog is a polypeptidethat has sequence similarity to a reference polypeptide, and thatcarries out one or more of the biochemical or physiological function(s)of the reference polypeptide. A functional homolog and the referencepolypeptide may be natural occurring polypeptides, and the sequencesimilarity may be due to convergent or divergent evolutionary events. Assuch, functional homologs are sometimes designated in the literature ashomologs, or orthologs, or paralogs. Variants of a naturally occurringfunctional homolog, such as polypeptides encoded by mutants of a wildtype coding sequence, may themselves be functional homologs. Functionalhomologs can also be created via site-directed mutagenesis of the codingsequence for a low nitrogen tolerance-modulating polypeptide, or bycombining domains from the coding sequences for differentnaturally-occurring low nitrogen tolerance-modulating polypeptides(“domain swapping”). The term “functional homolog” is sometimes appliedto the nucleic acid that encodes a functionally homologous polypeptide.

Functional homologs can be identified by analysis of nucleotide andpolypeptide sequence alignments. For example, performing a query on adatabase of nucleotide or polypeptide sequences can identify homologs oflow nitrogen tolerance-modulating polypeptides. Sequence analysis caninvolve BLAST, Reciprocal BLAST, or PSI-BLAST analysis of nonredundantdatabases using a low nitrogen tolerance-modulating polypeptide aminoacid sequence as the reference sequence. Amino acid sequence is, in someinstances, deduced from the nucleotide sequence. Those polypeptides inthe database that have greater than 20% sequence identity are candidatesfor further evaluation for suitability as a low nitrogentolerance-modulating polypeptide. Amino acid sequence similarity allowsfor conservative amino acid substitutions, such as substitution of onehydrophobic residue for another or substitution of one polar residue foranother. If desired, manual inspection of such candidates can be carriedout in order to narrow the number of candidates to be further evaluated.Manual inspection can be performed by selecting those candidates thatappear to have domains present in low nitrogen tolerance-modulatingpolypeptides, e.g., conserved functional domains.

Conserved regions can be identified by locating a region within theprimary amino acid sequence of a low nitrogen tolerance-modulatingpolypeptide that is a repeated sequence, forms some secondary structure(e.g., helices and beta sheets), establishes positively or negativelycharged domains, or represents a protein motif or domain. See, e.g., thePfam web site describing consensus sequences for a variety of proteinmotifs and domains on the World Wide Web at sanger.ac.uk/Software/Pfam/and pfam.janelia.org/. A description of the information included at thePfam database is described in Sonnhammer et al. (1998) Nucl. Acids Res.,26:320-322; Sonnhammer et al. (1997) Proteins, 28:405-420; and Batemanet al. (1999) Nucl. Acids Res., 27:260-262. Conserved regions also canbe determined by aligning sequences of the same or related polypeptidesfrom closely related species. Closely related species preferably arefrom the same family. In some embodiments, alignment of sequences fromtwo different species is adequate.

Typically, polypeptides that exhibit at least about 40% amino acidsequence identity are useful to identify conserved regions. Conservedregions of related polypeptides exhibit at least 20% amino acid sequenceidentity (e.g., at least 50%, at least 60%, at least 70%, at least 80%,or at least 90% amino acid sequence identity). In some embodiments, aconserved region exhibits at least 92%, 94%, 96%, 98%, or 99% amino acidsequence identity.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:3 are provided in FIG. 1 and in theSequence Listing. Such functional homologs include SEQ ID NO:4, SEQ IDNO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ IDNO:16, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ IDNO:22, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ IDNO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:36, SEQ ID NO:38, SEQ IDNO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ IDNO:44, SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:47. In some cases, afunctional homolog of SEQ ID NO:3 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:3.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:49 are provided in FIG. 2 and in theSequence Listing. Such functional homologs include SEQ ID NO:51, SEQ IDNO:53, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ IDNO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ ID NO:67, SEQ IDNO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:72, SEQ ID NO:73, and SEQID NO:75. In some cases, a functional homolog of SEQ ID NO:49 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:49.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:77 are provided in FIG. 3 and in theSequence Listing. Such functional homologs include SEQ ID NO:78, SEQ IDNO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:85, SEQ ID NO:87, SEQ IDNO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:93, SEQ ID NO:95, andCeresAnnot: 839064 (SEQ ID NO:1479). In some cases, a functional homologof SEQ ID NO:77 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:77.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:100 are provided in FIG. 4 and in theSequence Listing. Such functional homologs include SEQ ID NO:101, SEQ IDNO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:110, SEQID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQ ID NO:116, SEQ ID NO:117,SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120, SEQ ID NO:121, SEQ IDNO:122, SEQ ID NO:123, SEQ ID NO:125, SEQ ID NO:126, SEQ ID NO:128, SEQID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQ ID NO:132, SEQ ID NO:133,SEQ ID NO:134, SEQ ID NO:135, SEQ ID NO:137, SEQ ID NO:139, SEQ IDNO:141, SEQ ID NO:142, SEQ ID NO:144, SEQ ID NO:145, SEQ ID NO:146, SEQID NO:147, SEQ ID NO:148, SEQ ID NO:149, and SEQ ID NO:150. In somecases, a functional homolog of SEQ ID NO:100 has an amino acid sequencewith at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:100.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:152 are provided in FIG. 5 and in theSequence Listing. Such functional homologs include SEQ ID NO:154, SEQ IDNO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ ID NO:162, and SEQ ID NO:164.In some cases, a functional homolog of SEQ ID NO:152 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:152.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:166 are provided in FIG. 6 and in theSequence Listing. Such functional homologs include SEQ ID NO:168, SEQ IDNO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ ID NO:177, SEQ ID NO:179, SEQID NO:181, SEQ ID NO:182, SEQ ID NO:183, and SEQ ID NO:184. In somecases, a functional homolog of SEQ ID NO:166 has an amino acid sequencewith at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:166.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:186 are provided in FIG. 7 and in theSequence Listing. Such functional homologs include SEQ ID NO:188, SEQ IDNO:190, SEQ ID NO:191, SEQ ID NO:193, SEQ ID NO:194, SEQ ID NO:196, SEQID NO:197, SEQ ID NO:199, SEQ ID NO:201, SEQ ID NO:203, SEQ ID NO:204,SEQ ID NO:205, and SEQ ID NO:206. In some cases, a functional homolog ofSEQ ID NO:186 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:186.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:208 are provided in FIG. 8 and in theSequence Listing. Such functional homologs include SEQ ID NO:209, SEQ IDNO:210, SEQ ID NO:214, and SEQ ID NO:216. In some cases, a functionalhomolog of SEQ ID NO:208 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:208.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:218 are provided in FIG. 9 and in theSequence Listing. Such functional homologs include SEQ ID NO:220, SEQ IDNO:222, SEQ ID NO:223, SEQ ID NO:225, SEQ ID NO:227, SEQ ID NO:229, SEQID NO:230, SEQ ID NO:231, SEQ ID NO:232, SEQ ID NO:1039, SEQ ID NO:1049,and SEQ ID NO:1052. In some cases, a functional homolog of SEQ ID NO:218has an amino acid sequence with at least 20% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% sequence identity, to the amino acid sequence set forth in SEQ IDNO:218.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:234 are provided in FIG. 10 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:236,SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:241, SEQ ID NO:242, SEQ IDNO:243, and SEQ ID NO:244. In some cases, a functional homolog of SEQ IDNO:234 has an amino acid sequence with at least 20% sequence identity,e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, or 99% sequence identity, to the amino acid sequence set forth inSEQ ID NO:234.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:246 are provided in FIG. 11 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:248,SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ ID NO:255, SEQ IDNO:257, SEQ ID NO:259, SEQ ID NO:260, SEQ ID NO:262, SEQ ID NO:264, SEQID NO:265, SEQ ID NO:267, SEQ ID NO:268, SEQ ID NO:270, SEQ ID NO:272,SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:277, SEQ ID NO:279, SEQ IDNO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:286, SEQ ID NO:287, SEQID NO:288, SEQ ID NO:290, SEQ ID NO:291, SEQ ID NO:292, SEQ ID NO:293,SEQ ID NO:296, and SEQ ID NO:298. In some cases, a functional homolog ofSEQ ID NO:246 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:246.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:300 are provided in FIG. 12 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:302,SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:308, SEQ ID NO:310, SEQ IDNO:312, SEQ ID NO:314, SEQ ID NO:316, SEQ ID NO:318, SEQ ID NO:319, SEQID NO:320, SEQ ID NO:321, SEQ ID NO:322, SEQ ID NO:323, SEQ ID NO:325,SEQ ID NO:327, and SEQ ID NO:329. In some cases, a functional homolog ofSEQ ID NO:300 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:300.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:332 are provided in FIG. 13 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:332,SEQ ID NO:334, SEQ ID NO:335, SEQ ID NO:336, SEQ ID NO:338, SEQ IDNO:339, SEQ ID NO:341, SEQ ID NO:342, SEQ ID NO:343, SEQ ID NO:344, SEQID NO:345, SEQ ID NO:346, SEQ ID NO:347, SEQ ID NO:348, SEQ ID NO:349,SEQ ID NO:351, SEQ ID NO:352, SEQ ID NO:353, SEQ ID NO:354, SEQ IDNO:355, SEQ ID NO:356, SEQ ID NO:357, SEQ ID NO:358, SEQ ID NO:359, SEQID NO:360, SEQ ID NO:362, SEQ ID NO:363, SEQ ID NO:364, SEQ ID NO:365,SEQ ID NO:366, SEQ ID NO:2541, SEQ ID NO:2542, SEQ ID NO:2543, SEQ IDNO:2544, SEQ ID NO:2546, SEQ ID NO:2548, SEQ ID NO:2549, SEQ ID NO:2550,SEQ ID NO:2551, SEQ ID NO:2552, and SEQ ID NO:2553. In some cases, afunctional homolog of SEQ ID NO:332 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:332.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:368 are provided in FIG. 14 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:369,SEQ ID NO:370, SEQ ID NO:371, SEQ ID NO:372, SEQ ID NO:373, SEQ IDNO:374, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQ ID NO:382, SEQID NO:384, SEQ ID NO:386, SEQ ID NO:388, SEQ ID NO:390, SEQ ID NO:392,SEQ ID NO:394, SEQ ID NO:396, SEQ ID NO:398, SEQ ID NO:399, SEQ IDNO:401, SEQ ID NO:403, SEQ ID NO:404, SEQ ID NO:406, SEQ ID NO:408, SEQID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416, SEQ ID NO:418,SEQ ID NO:419, SEQ ID NO:420, SEQ ID NO:422, SEQ ID NO:423, SEQ IDNO:425, SEQ ID NO:427, SEQ ID NO:428, SEQ ID NO:430, SEQ ID NO:432, SEQID NO:433, SEQ ID NO:434, SEQ ID NO:435, SEQ ID NO:436, SEQ ID NO:437,SEQ ID NO:438, SEQ ID NO:439, SEQ ID NO:440, SEQ ID NO:441, SEQ IDNO:444, SEQ ID NO:445, SEQ ID NO:446, SEQ ID NO:447, SEQ ID NO:448, SEQID NO:449, SEQ ID NO:450, SEQ ID NO:451, SEQ ID NO:452, SEQ ID NO:453,SEQ ID NO:454, SEQ ID NO:455, SEQ ID NO:456, SEQ ID NO:458, SEQ IDNO:459, SEQ ID NO:461, SEQ ID NO:463, SEQ ID NO:465, SEQ ID NO:467, SEQID NO:469, SEQ ID NO:471, SEQ ID NO:473, SEQ ID NO:474, SEQ ID NO:475,SEQ ID NO:477, SEQ ID NO:479, SEQ ID NO:481, SEQ ID NO:483, SEQ IDNO:485, SEQ ID NO:487, SEQ ID NO:488, SEQ ID NO:489, SEQ ID NO:490, SEQID NO:491, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NO:495, SEQ ID NO:496,SEQ ID NO:497, SEQ ID NO:498, SEQ ID NO:499, SEQ ID NO:500, SEQ IDNO:501, SEQ ID NO:502, SEQ ID NO:504, SEQ ID NO:505, SEQ ID NO:506, SEQID NO:507, and SEQ ID NO:508. In some cases, a functional homolog of SEQID NO:368 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:368.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:510 are provided in FIG. 15 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:511,SEQ ID NO:513, SEQ ID NO:515, SEQ ID NO:517, SEQ ID NO:521, SEQ IDNO:523, SEQ ID NO:525, SEQ ID NO:527, SEQ ID NO:529, SEQ ID NO:530, andSEQ ID NO:531. In some cases, a functional homolog of SEQ ID NO:510 hasan amino acid sequence with at least 20% sequence identity, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:510.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:533 are provided in FIG. 16 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:535,SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:539, SEQ ID NO:541, SEQ IDNO:542, SEQ ID NO:543, SEQ ID NO:544, SEQ ID NO:545, SEQ ID NO:546, SEQID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:552, SEQ ID NO:553,and SEQ ID NO:554. In some cases, a functional homolog of SEQ ID NO:533has an amino acid sequence with at least 20% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% sequence identity, to the amino acid sequence set forth in SEQ IDNO:533.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:558 are provided in FIG. 17 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:559,SEQ ID NO:560, SEQ ID NO:561, SEQ ID NO:562, SEQ ID NO:563, SEQ IDNO:564, SEQ ID NO:565, SEQ ID NO:566, SEQ ID NO:567, SEQ ID NO:569, SEQID NO:571, SEQ ID NO:572, SEQ ID NO:573, SEQ ID NO:575, SEQ ID NO:576,SEQ ID NO:577, SEQ ID NO:578, SEQ ID NO:579, SEQ ID NO:581, SEQ IDNO:583, SEQ ID NO:584, SEQ ID NO:585, SEQ ID NO:586, SEQ ID NO:588, SEQID NO:589, SEQ ID NO:590, and SEQ ID NO:591. In some cases, a functionalhomolog of SEQ ID NO:558 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:558.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:593 are provided in FIG. 18 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:595,SEQ ID NO:597, SEQ ID NO:599, SEQ ID NO:601, SEQ ID NO:603, SEQ IDNO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:610, and SEQ ID NO:611.In some cases, a functional homolog of SEQ ID NO:593 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:593.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:613 are provided in FIG. 19 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:615,SEQ ID NO:617, SEQ ID NO:618, SEQ ID NO:620, SEQ ID NO:622, SEQ IDNO:624, SEQ ID NO:626, SEQ ID NO:628, SEQ ID NO:630, SEQ ID NO:632, SEQID NO:634, SEQ ID NO:636, SEQ ID NO:638, SEQ ID NO:640, SEQ ID NO:642,SEQ ID NO:643, and SEQ ID NO:644. In some cases, a functional homolog ofSEQ ID NO:613 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:613.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:646 are provided in FIG. 20 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:648,SEQ ID NO:650, SEQ ID NO:652, SEQ ID NO:654, SEQ ID NO:656, SEQ IDNO:658, SEQ ID NO:660, SEQ ID NO:662, SEQ ID NO:664, SEQ ID NO:666, SEQID NO:668, SEQ ID NO:670, SEQ ID NO:672, SEQ ID NO:674, SEQ ID NO:676,SEQ ID NO:678, SEQ ID NO:679, SEQ ID NO:680, SEQ ID NO:681, SEQ IDNO:682, SEQ ID NO:683, and SEQ ID NO:685. In some cases, a functionalhomolog of SEQ ID NO:646 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:646.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:687 are provided in FIG. 21 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:689,SEQ ID NO:691, SEQ ID NO:693, SEQ ID NO:694, SEQ ID NO:696, SEQ IDNO:697, SEQ ID NO:699, SEQ ID NO:701, SEQ ID NO:703, SEQ ID NO:705, SEQID NO:706, SEQ ID NO:708, SEQ ID NO:710, SEQ ID NO:712, SEQ ID NO:714,SEQ ID NO:716, SEQ ID NO:718, SEQ ID NO:720, SEQ ID NO:721, SEQ IDNO:722, SEQ ID NO:723, SEQ ID NO:724, SEQ ID NO:725, SEQ ID NO:726, SEQID NO:727, and SEQ ID NO:728. In some cases, a functional homolog of SEQID NO:687 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:687.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:730 are provided in FIG. 22 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:732,SEQ ID NO:733, SEQ ID NO:735, SEQ ID NO:737, SEQ ID NO:738, and SEQ IDNO:742. In some cases, a functional homolog of SEQ ID NO:730 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:730.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:746 are provided in FIG. 23 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:748,SEQ ID NO:750, SEQ ID NO:751, SEQ ID NO:753, SEQ ID NO:755, SEQ IDNO:757, SEQ ID NO:758, SEQ ID NO:760, SEQ ID NO:761, SEQ ID NO:762, SEQID NO:763, SEQ ID NO:765, and SEQ ID NO:767. In some cases, a functionalhomolog of SEQ ID NO:746 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:746.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:769 are provided in FIG. 24 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:771,SEQ ID NO:773, SEQ ID NO:775, SEQ ID NO:777, SEQ ID NO:779, SEQ IDNO:781, SEQ ID NO:783, SEQ ID NO:785, SEQ ID NO:787, SEQ ID NO:789, andSEQ ID NO:790. In some cases, a functional homolog of SEQ ID NO:769 hasan amino acid sequence with at least 20% sequence identity, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:769.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:792 are provided in FIG. 25 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:794,SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:799, SEQ ID NO:801, SEQ IDNO:803, SEQ ID NO:805, SEQ ID NO:807, SEQ ID NO:808, SEQ ID NO:810, SEQID NO:812, SEQ ID NO:814, SEQ ID NO:816, SEQ ID NO:818, SEQ ID NO:819,SEQ ID NO:820, SEQ ID NO:821, and SEQ ID NO:822. In some cases, afunctional homolog of SEQ ID NO:792 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:792.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:824 are provided in FIG. 26 and inthe Sequence Listing. Such functional homologs include, but not limitedto, SEQ ID NO:826, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ IDNO:1710, SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1714, SEQ ID NO:1715,and SEQ ID NO:1716. In some cases, a functional homolog of SEQ ID NO:824has an amino acid sequence with at least 20% sequence identity, e.g.,50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% sequence identity, to the amino acid sequence set forth in SEQ IDNO:824.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:828 are provided in FIG. 27 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:830,SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:836, SEQ ID NO:837, SEQ IDNO:838, SEQ ID NO:839, SEQ ID NO:840, SEQ ID NO:842, SEQ ID NO:844, SEQID NO:845, SEQ ID NO:846, SEQ ID NO:847, SEQ ID NO:848, SEQ ID NO:849,SEQ ID NO:850, and SEQ ID NO:851. In some cases, a functional homolog ofSEQ ID NO:828 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:828.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:855 are provided in FIG. 28 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:856,SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:862, SEQ ID NO:864, SEQ IDNO:866, SEQ ID NO:868, SEQ ID NO:870, SEQ ID NO:872, SEQ ID NO:874, SEQID NO:876, SEQ ID NO:878, SEQ ID NO:880, SEQ ID NO:882, SEQ ID NO:884,SEQ ID NO:885, SEQ ID NO:886, SEQ ID NO:887, SEQ ID NO:888, and SEQ IDNO:889. In some cases, a functional homolog of SEQ ID NO:855 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:855.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:891 are provided in FIG. 29 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:893,SEQ ID NO:894, SEQ ID NO:895, SEQ ID NO:896, SEQ ID NO:898, SEQ IDNO:900, SEQ ID NO:901, SEQ ID NO:902, SEQ ID NO:903, SEQ ID NO:904, SEQID NO:905, SEQ ID NO:907, SEQ ID NO:908, SEQ ID NO:909, SEQ ID NO:910,SEQ ID NO:911, SEQ ID NO:912, SEQ ID NO:913, SEQ ID NO:914, and SEQ IDNO:915. In some cases, a functional homolog of SEQ ID NO:891 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:891.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:917 are provided in FIG. 30 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:919,SEQ ID NO:921, SEQ ID NO:923, SEQ ID NO:925, SEQ ID NO:927, SEQ IDNO:929, SEQ ID NO:931, SEQ ID NO:933, SEQ ID NO:935, SEQ ID NO:937, SEQID NO:939, and SEQ ID NO:940. In some cases, a functional homolog of SEQID NO:917 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:917.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:944 are provided in FIG. 31 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:946,SEQ ID NO:947, SEQ ID NO:948, SEQ ID NO:950, SEQ ID NO:952, SEQ IDNO:954, SEQ ID NO:956, SEQ ID NO:958, SEQ ID NO:960, SEQ ID NO:962, SEQID NO:964, SEQ ID NO:966, SEQ ID NO:967, SEQ ID NO:968, SEQ ID NO:969,SEQ ID NO:970, SEQ ID NO:972, and SEQ ID NO:974. In some cases, afunctional homolog of SEQ ID NO:944 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:944.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:976 are provided in FIG. 32 and inthe Sequence Listing. Such functional homologs include, but not limitedto, SEQ ID NO:978 and SEQ ID NO:980. In some cases, a functional homologof SEQ ID NO:976 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:976.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:982 are provided in FIG. 33 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:984,SEQ ID NO:985, SEQ ID NO:986, SEQ ID NO:987, SEQ ID NO:988, SEQ IDNO:989, SEQ ID NO:990, SEQ ID NO:991, SEQ ID NO:992, SEQ ID NO:993, SEQID NO:995, SEQ ID NO:996, SEQ ID NO:998, SEQ ID NO:1000, SEQ ID NO:1001,SEQ ID NO:1003, SEQ ID NO:1005, SEQ ID NO:1007, SEQ ID NO:1008, SEQ IDNO:1009, SEQ ID NO:1011, SEQ ID NO:1013, SEQ ID NO:1015, SEQ ID NO:1016,SEQ ID NO:1018, SEQ ID NO:1019, SEQ ID NO:1021, SEQ ID NO:1023, SEQ IDNO:1025, SEQ ID NO:1026, SEQ ID NO:1027, SEQ ID NO:1028, SEQ ID NO:1029,SEQ ID NO:1030, SEQ ID NO:1031, SEQ ID NO:1032, and SEQ ID NO:1033. Insome cases, a functional homolog of SEQ ID NO:982 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:982.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1054 are provided in FIG. 34 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1055,SEQ ID NO:1057, SEQ ID NO:1058, SEQ ID NO:1059, SEQ ID NO:1061, SEQ IDNO:1063, SEQ ID NO:1065, SEQ ID NO:1067, SEQ ID NO:1068, SEQ ID NO:1070,SEQ ID NO:1071, SEQ ID NO:1072, SEQ ID NO:1074, SEQ ID NO:1075, SEQ IDNO:1076, SEQ ID NO:1077, SEQ ID NO:1078, SEQ ID NO:1080, SEQ ID NO:1082,SEQ ID NO:1083, SEQ ID NO:1085, SEQ ID NO:1086, SEQ ID NO:1087, SEQ IDNO:1088, SEQ ID NO:1089, SEQ ID NO:1090, SEQ ID NO:1091, SEQ ID NO:1092,SEQ ID NO:1093, SEQ ID NO:1094, SEQ ID NO:1095, and SEQ ID NO:1097. Insome cases, a functional homolog of SEQ ID NO:1054 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:1054.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1099 are provided in FIG. 35 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1101,SEQ ID NO:1103, SEQ ID NO:1104, SEQ ID NO:1105, SEQ ID NO:1106, SEQ IDNO:1108, SEQ ID NO:1109, and SEQ ID NO:1110. In some cases, a functionalhomolog of SEQ ID NO:1099 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:1099.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1112 are provided in FIG. 36 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1113and SEQ ID NO:1114. In some cases, a functional homolog of SEQ IDNO:1112 has an amino acid sequence with at least 20% sequence identity,e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, or 99% sequence identity, to the amino acid sequence set forth inSEQ ID NO:1112.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1116 are provided in FIG. 37 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1118,SEQ ID NO:1120, SEQ ID NO:1122, SEQ ID NO:1123, SEQ ID NO:1125, SEQ IDNO:1126, SEQ ID NO:1128, SEQ ID NO:1129, SEQ ID NO:1131, SEQ ID NO:1132,SEQ ID NO:1133, SEQ ID NO:1134, SEQ ID NO:1136, SEQ ID NO:1138, SEQ IDNO:1140, SEQ ID NO:1141, SEQ ID NO:1142, SEQ ID NO:1143, SEQ ID NO:1144,SEQ ID NO:1145, SEQ ID NO:1147, SEQ ID NO:1149, SEQ ID NO:1151, SEQ IDNO:1153, and SEQ ID NO:1155. In some cases, a functional homolog of SEQID NO:1116 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1116.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1159 are provided in FIG. 38 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1161,SEQ ID NO:1162, SEQ ID NO:1163, and SEQ ID NO:1164. In some cases, afunctional homolog of SEQ ID NO:1159 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1159.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1166 are provided in FIG. 39 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1167,SEQ ID NO:1169, SEQ ID NO:1171, SEQ ID NO:1173, SEQ ID NO:1175, SEQ IDNO:1177, SEQ ID NO:1179, SEQ ID NO:1180, SEQ ID NO:1182, and SEQ IDNO:1183. In some cases, a functional homolog of SEQ ID NO:1166 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1166.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1185 are provided in FIG. 40 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1187,SEQ ID NO:1189, SEQ ID NO:1190, SEQ ID NO:1191, and SEQ ID NO:1192. Insome cases, a functional homolog of SEQ ID NO:1185 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:1185.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1194 are provided in FIG. 41 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1196,SEQ ID NO:1198, SEQ ID NO:1200, SEQ ID NO:1202, SEQ ID NO:1203, SEQ IDNO:1204, SEQ ID NO:1205, SEQ ID NO:1206, SEQ ID NO:1207, and SEQ IDNO:1208. In some cases, a functional homolog of SEQ ID NO:1194 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1194.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1210 are provided in FIG. 42 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1211,SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1216, SEQ ID NO:1218, SEQ IDNO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1226, SEQ ID NO:1228,SEQ ID NO:1229, SEQ ID NO:1230, SEQ ID NO:1232, SEQ ID NO:1233, SEQ IDNO:1234, SEQ ID NO:1235, SEQ ID NO:1236, SEQ ID NO:1237, SEQ ID NO:1238,SEQ ID NO:1239, SEQ ID NO:1240, SEQ ID NO:1241, SEQ ID NO:1242, SEQ IDNO:1243, SEQ ID NO:1244, SEQ ID NO:1245, SEQ ID NO:1246, SEQ ID NO:1247,SEQ ID NO:1248, SEQ ID NO:1249, SEQ ID NO:1251, SEQ ID NO:1253, SEQ IDNO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261, SEQ ID NO:1263,SEQ ID NO:1264, SEQ ID NO:1265, SEQ ID NO:1266, SEQ ID NO:1267, SEQ IDNO:1268, SEQ ID NO:1269, SEQ ID NO:1270, SEQ ID NO:1271, and SEQ IDNO:1272. In some cases, a functional homolog of SEQ ID NO:1210 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1210.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1274 are provided in FIG. 43 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1276,SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1281, SEQ ID NO:1282, SEQ IDNO:1284, SEQ ID NO:1285, SEQ ID NO:1287, SEQ ID NO:1289, SEQ ID NO:1291,SEQ ID NO:1293, SEQ ID NO:1294, SEQ ID NO:1295, SEQ ID NO:1296, SEQ IDNO:1297, SEQ ID NO:1298, and SEQ ID NO:1300. In some cases, a functionalhomolog of SEQ ID NO:1274 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:1274.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1302 are provided in FIG. 44 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1303,SEQ ID NO:1305, SEQ ID NO:1307, SEQ ID NO:1309, SEQ ID NO:1311, SEQ IDNO:1312, SEQ ID NO:1313, SEQ ID NO:1314, SEQ ID NO:1315, SEQ ID NO:1317,SEQ ID NO:1318, SEQ ID NO:1319, SEQ ID NO:1320, SEQ ID NO:1321, SEQ IDNO:1322, SEQ ID NO:1323, SEQ ID NO:1324, SEQ ID NO:1325, SEQ ID NO:1326,SEQ ID NO:1327, SEQ ID NO:1328, SEQ ID NO:1330, SEQ ID NO:1331, SEQ IDNO:1333, SEQ ID NO:1334, SEQ ID NO:1335, SEQ ID NO:1336, SEQ ID NO:1337,SEQ ID NO:1338, SEQ ID NO:1339, and SEQ ID NO:1340. In some cases, afunctional homolog of SEQ ID NO:1302 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1302.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1342 are provided in FIG. 45 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1344,SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ ID NO:1352, SEQ IDNO:1354, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1358, SEQ ID NO:1360,SEQ ID NO:1361, SEQ ID NO:1362, SEQ ID NO:1363, SEQ ID NO:1364, SEQ IDNO:1366, SEQ ID NO:1367, SEQ ID NO:1369, SEQ ID NO:1370, SEQ ID NO:1371,SEQ ID NO:1372, SEQ ID NO:1373, SEQ ID NO:1374, SEQ ID NO:1375, SEQ IDNO:1376, SEQ ID NO:1377, SEQ ID NO:1378, SEQ ID NO:1379, SEQ ID NO:1380,SEQ ID NO:1381, SEQ ID NO:1382, and SEQ ID NO:1383. In some cases, afunctional homolog of SEQ ID NO:1342 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1342.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1385 are provided in FIG. 46 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1387,SEQ ID NO:1389, SEQ ID NO:1390, SEQ ID NO:1391, SEQ ID NO:1393, SEQ IDNO:1394, SEQ ID NO:1395, SEQ ID NO:1396, SEQ ID NO:1398, SEQ ID NO:1400,SEQ ID NO:1401, SEQ ID NO:1402, SEQ ID NO:1403, SEQ ID NO:1404, SEQ IDNO:1405, and SEQ ID NO:1407. In some cases, a functional homolog of SEQID NO:1385 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1385.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1409 are provided in FIG. 47 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1411,SEQ ID NO:1413, SEQ ID NO:1415, SEQ ID NO:1417, SEQ ID NO:1418, SEQ IDNO:1419, SEQ ID NO:1421, SEQ ID NO:1423, SEQ ID NO:1424, SEQ ID NO:1425,and SEQ ID NO:1426. In some cases, a functional homolog of SEQ IDNO:1409 has an amino acid sequence with at least 20% sequence identity,e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, or 99% sequence identity, to the amino acid sequence set forth inSEQ ID NO:1409.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1428 are provided in FIG. 48 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1430,SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1436, SEQ ID NO:1439, SEQ IDNO:1442, SEQ ID NO:1444, SEQ ID NO:1446, SEQ ID NO:1448, SEQ ID NO:1450,SEQ ID NO:1452, SEQ ID NO:1453, SEQ ID NO:1454, SEQ ID NO:1455, SEQ IDNO:1456, SEQ ID NO:1457, SEQ ID NO:1458, and SEQ ID NO:1459. In somecases, a functional homolog of SEQ ID NO:1428 has an amino acid sequencewith at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1428.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1463 are provided in FIG. 49 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1465,SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ ID NO:1473, SEQ IDNO:1474, SEQ ID NO:1475, SEQ ID NO:1476, and SEQ ID NO:1477. In somecases, a functional homolog of SEQ ID NO:1463 has an amino acid sequencewith at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1463.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1491 are provided in FIG. 50 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1493,SEQ ID NO:1495, SEQ ID NO:1497, SEQ ID NO:1499, SEQ ID NO:1501, SEQ IDNO:1503, SEQ ID NO:1504, SEQ ID NO:1505, SEQ ID NO:1506, and SEQ IDNO:1508. In some cases, a functional homolog of SEQ ID NO:1491 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1491.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1510 are provided in FIG. 51 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1512,SEQ ID NO:1514, SEQ ID NO:1516, SEQ ID NO:1518, SEQ ID NO:1520, SEQ IDNO:1522, and SEQ ID NO:1523. In some cases, a functional homolog of SEQID NO:1510 has an amino acid sequence with at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:1510.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1525 are provided in FIG. 52 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1527,SEQ ID NO:1529, SEQ ID NO:1530, SEQ ID NO:1532, SEQ ID NO:1534, and SEQID NO:1535. In some cases, a functional homolog of SEQ ID NO:1525 has anamino acid sequence with at least 20% sequence identity, e.g., 50%, 52%,56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1525.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1537 are provided in FIG. 53 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1539,SEQ ID NO:1540, SEQ ID NO:1541, SEQ ID NO:1543, SEQ ID NO:1545, SEQ IDNO:1547, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552, SEQ ID NO:2386,SEQ ID NO:2388, SEQ ID NO:2390, SEQ ID NO:2391, and SEQ ID NO:2392. Insome cases, a functional homolog of SEQ ID NO:1537 has an amino acidsequence with at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%,61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequenceidentity, to the amino acid sequence set forth in SEQ ID NO:1537.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1554 are provided in FIG. 54 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1555,SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ ID NO:1563, SEQ IDNO:1565, SEQ ID NO:1567, SEQ ID NO:1569, SEQ ID NO:1571, SEQ ID NO:1572,SEQ ID NO:1573, SEQ ID NO:1574, and SEQ ID NO:1575. In some cases, afunctional homolog of SEQ ID NO:1554 has an amino acid sequence with atleast 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1554.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1577 are provided in FIG. 55 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:1035,SEQ ID NO:1036, SEQ ID NO:1037, SEQ ID NO:1040, SEQ ID NO:1041, SEQ IDNO:1043, SEQ ID NO:1044, SEQ ID NO:1046, SEQ ID NO:1047, SEQ ID NO:1048,SEQ ID NO:1050, SEQ ID NO:1440, SEQ ID NO:1480, SEQ ID NO:1481, SEQ IDNO:1482, SEQ ID NO:1483, SEQ ID NO:1484, SEQ ID NO:1485, SEQ ID NO:1486,SEQ ID NO:1487, SEQ ID NO:1488, SEQ ID NO:1578, SEQ ID NO:1580, SEQ IDNO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588, SEQ ID NO:1590,SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1596, SEQ ID NO:1598, SEQ IDNO:1599, SEQ ID NO:1601, SEQ ID NO:1602, SEQ ID NO:1605, SEQ ID NO:1607,SEQ ID NO:1608, SEQ ID NO:1609, SEQ ID NO:1611, SEQ ID NO:1613, SEQ IDNO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1621, SEQ ID NO:1622,SEQ ID NO:1623, SEQ ID NO:1624, SEQ ID NO:1625, SEQ ID NO:1627, SEQ IDNO:1629, SEQ ID NO:1631, SEQ ID NO:1633, SEQ ID NO:1635, SEQ ID NO:1637,SEQ ID NO:1639, SEQ ID NO:1643, SEQ ID NO:1645, SEQ ID NO:1648, SEQ IDNO:1649, SEQ ID NO:1651, and SEQ ID NO:1653. In some cases, a functionalhomolog of SEQ ID NO:1577 has an amino acid sequence with at least 20%sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%,85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to the amino acidsequence set forth in SEQ ID NO:1577.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:1437 are provided in FIG. 56 and inthe Sequence Listing. Such functional homologs include SEQ ID NO:173,SEQ ID NO:212, SEQ ID NO:361, SEQ ID NO:421, SEQ ID NO:443, SEQ IDNO:740, SEQ ID NO:744, SEQ ID NO:942, and SEQ ID NO:1461. In some cases,a functional homolog of SEQ ID NO:1437 has an amino acid sequence withat least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:1437.

Examples of amino acid sequences of functional homologs of thepolypeptide set forth in SEQ ID NO:97 are provided in FIG. 57 and in theSequence Listing. Such functional homologs include SEQ ID NO:2010, SEQID NO:2011, SEQ ID NO:2013, SEQ ID NO:2015, SEQ ID NO:2017. In somecases, a functional homolog of SEQ ID NO:97 has an amino acid sequencewith at least 20% sequence identity, e.g., 50%, 52%, 56%, 59%, 61%, 65%,70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to theamino acid sequence set forth in SEQ ID NO:97.

The identification of conserved regions in a low nitrogentolerance-modulating polypeptide facilitates production of variants oflow nitrogen tolerance-modulating polypeptides. Variants of low nitrogentolerance-modulating polypeptides typically have 10 or fewerconservative amino acid substitutions within the primary amino acidsequence, e.g., 7 or fewer conservative amino acid substitutions, 5 orfewer conservative amino acid substitutions, or between 1 and 5conservative substitutions. A useful variant polypeptide can beconstructed based on one of the alignments set forth in FIG. 1-57 and/orhomologs identified in the Sequence Listing. Such a polypeptide includesthe conserved regions, arranged in the order depicted in the Figure fromamino-terminal end to carboxy-terminal end. Such a polypeptide may alsoinclude zero, one, or more than one amino acid in positions marked bydashes. When no amino acids are present at positions marked by dashes,the length of such a polypeptide is the sum of the amino acid residuesin all conserved regions. When amino acids are present at all positionsmarked by dashes, such a polypeptide has a length that is the sum of theamino acid residues in all conserved regions and all dashes.

C. Functional Homologs Identified by HMMER

In some embodiments, useful low nitrogen tolerance-modulatingpolypeptides include those that fit a Hidden Markov Model based on thepolypeptides set forth in any one of FIGS. 1-57. A Hidden Markov Model(HMM) is a statistical model of a consensus sequence for a group offunctional homologs. See, Durbin et al. (1998) Biological SequenceAnalysis: Probabilistic Models of Proteins and Nucleic Acids, CambridgeUniversity Press, Cambridge, UK. An HMM is generated by the programHMMER 2.3.2 with default program parameters, using the sequences of thegroup of functional homologs as input. The multiple sequence alignmentis generated by ProbCons (Do et al. (2005) Genome Res., 15(2):330-40)version 1.11 using a set of default parameters: -c, —consistency REPS of2; -ir, —iterative-refinement REPS of 100; -pre, —pre-training REPS of0. ProbCons is a public domain software program provided by StanfordUniversity.

The default parameters for building an HMM (hmmbuild) are as follows:the default “architecture prior” (archpri) used by MAP architectureconstruction is 0.85, and the default cutoff threshold (idlevel) used todetermine the effective sequence number is 0.62. HMMER 2.3.2 wasreleased Oct. 3, 2003 under a GNU general public license, and isavailable from various sources on the World Wide Web such ashmmer.janelia.org; hmmer.wustl.edu; and fr.com/hmmer232/. Hmmbuildoutputs the model as a text file.

The HMM for a group of functional homologs can be used to determine thelikelihood that a candidate low nitrogen tolerance-modulatingpolypeptide sequence is a better fit to that particular HMM than to anull HMM generated using a group of sequences that are not structurallyor functionally related. The likelihood that a candidate polypeptidesequence is a better fit to an HMM than to a null HMM is indicated bythe HMM bit score, a number generated when the candidate sequence isfitted to the HMM profile using the HMMER hmmsearch program. Thefollowing default parameters are used when running hmmsearch: thedefault E-value cutoff (E) is 10.0, the default bit score cutoff (T) isnegative infinity, the default number of sequences in a database (Z) isthe real number of sequences in the database, the default E-value cutofffor the per-domain ranked hit list (domE) is infinity, and the defaultbit score cutoff for the per-domain ranked hit list (domT) is negativeinfinity. A high HMM bit score indicates a greater likelihood that thecandidate sequence carries out one or more of the biochemical orphysiological function(s) of the polypeptides used to generate the HMM.A high HMM bit score is at least 20, and often is higher. Slightvariations in the HMM bit score of a particular sequence can occur dueto factors such as the order in which sequences are processed foralignment by multiple sequence alignment algorithms such as the ProbConsprogram. Nevertheless, such HMM bit score variation is minor.

The low nitrogen tolerance-modulating polypeptides discussed below fitthe indicated HMM with an HMM bit score greater than 20 (e.g., greaterthan 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, or 500). In someembodiments, the HMM bit score of a low nitrogen tolerance-modulatingpolypeptide discussed below is about 50%, 60%, 70%, 80%, 90%, or 95% ofthe HMM bit score of a functional homolog provided the Sequence Listingof this application. In some embodiments, a low nitrogentolerance-modulating polypeptide discussed below fits the indicated HMMwith an HMM bit score greater than 20, and has a domain indicative of alow nitrogen tolerance-modulating polypeptide. In some embodiments, alow nitrogen tolerance-modulating polypeptide discussed below fits theindicated HMM with an HMM bit score greater than 20, and has 70% orgreater sequence identity (e.g., 75%, 80%, 85%, 90%, 95%, or 100%sequence identity) to an amino acid sequence shown in any one of FIGS.1-57.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 800 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 1 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:3, SEQID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID NO:12, SEQ IDNO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:20, SEQ IDNO:21, SEQ ID NO:22, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:27, SEQ IDNO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ ID NO:35, SEQ ID NO:36, SEQ IDNO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ ID NO:41, SEQ ID NO:42, SEQ IDNO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ ID NO:46, and SEQ ID NO:47.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 2 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:49, SEQID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:56, SEQ ID NO:58, SEQ IDNO:60, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ ID NO:65, SEQ IDNO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:72, SEQ IDNO:73, and SEQ ID NO:75.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 540 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 3 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:77, SEQID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ ID NO:85, SEQ IDNO:87, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ ID NO:93, SEQ IDNO:95, and SEQ ID NO:1479.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 210 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 4 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:100,SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:104, SEQ ID NO:106, SEQ IDNO:108, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:113, SEQ ID NO:115, SEQID NO:116, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119, SEQ ID NO:120,SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ ID NO:125, SEQ IDNO:126, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQ ID NO:131, SEQID NO:132, SEQ ID NO:133, SEQ ID NO:134, SEQ ID NO:135, SEQ ID NO:137,SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:142, SEQ ID NO:144, SEQ IDNO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQ ID NO:149, andSEQ ID NO:150.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 90 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 5 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:152,SEQ ID NO:154, SEQ ID NO:156, SEQ ID NO:158, SEQ ID NO:160, SEQ IDNO:162, and SEQ ID NO:164.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 230 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 6 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:166,SEQ ID NO:168, SEQ ID NO:170, SEQ ID NO:172, SEQ ID NO:174, SEQ IDNO:177, SEQ ID NO:179, SEQ ID NO:181, SEQ ID NO:182, SEQ ID NO:183, andSEQ ID NO:184.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 90 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 7 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:186,SEQ ID NO:188, SEQ ID NO:190, SEQ ID NO:191, SEQ ID NO:193, SEQ IDNO:194, SEQ ID NO:196, SEQ ID NO:197, SEQ ID NO:199, SEQ ID NO:201, SEQID NO:203, SEQ ID NO:204, SEQ ID NO:205, and SEQ ID NO:206.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 380 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 8 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:208,SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:214, and SEQ ID NO:216.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 110 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 9 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:218,SEQ ID NO:220, SEQ ID NO:222, SEQ ID NO:223, SEQ ID NO:225, SEQ IDNO:227, SEQ ID NO:229, SEQ ID NO:230, SEQ ID NO:231, SEQ ID NO:232, SEQID NO:1039, SEQ ID NO:1049, and SEQ ID NO:1052.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 220 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 10 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:234,SEQ ID NO:236, SEQ ID NO:238, SEQ ID NO:239, SEQ ID NO:241, SEQ IDNO:242, SEQ ID NO:243, and SEQ ID NO:244.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 11 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:246,SEQ ID NO:248, SEQ ID NO:249, SEQ ID NO:251, SEQ ID NO:253, SEQ IDNO:255, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:260, SEQ ID NO:262, SEQID NO:264, SEQ ID NO:265, SEQ ID NO:267, SEQ ID NO:268, SEQ ID NO:270,SEQ ID NO:272, SEQ ID NO:274, SEQ ID NO:276, SEQ ID NO:277, SEQ IDNO:279, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQ ID NO:286, SEQID NO:287, SEQ ID NO:288, SEQ ID NO:290, SEQ ID NO:291, SEQ ID NO:292,SEQ ID NO:293, SEQ ID NO:296, and SEQ ID NO:298.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 950 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 12 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:300,SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ ID NO:308, SEQ IDNO:310, SEQ ID NO:312, SEQ ID NO:314, SEQ ID NO:316, SEQ ID NO:318, SEQID NO:319, SEQ ID NO:320, SEQ ID NO:321, SEQ ID NO:322, SEQ ID NO:323,SEQ ID NO:325, SEQ ID NO:327, and SEQ ID NO:329.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 460 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 13 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:332,SEQ ID NO:334, SEQ ID NO:335, SEQ ID NO:336, SEQ ID NO:338, SEQ IDNO:339, SEQ ID NO:341, SEQ ID NO:342, SEQ ID NO:343, SEQ ID NO:344, SEQID NO:345, SEQ ID NO:346, SEQ ID NO:347, SEQ ID NO:348, SEQ ID NO:349,SEQ ID NO:351, SEQ ID NO:352, SEQ ID NO:353, SEQ ID NO:354, SEQ IDNO:355, SEQ ID NO:356, SEQ ID NO:357, SEQ ID NO:358, SEQ ID NO:359, SEQID NO:360, SEQ ID NO:362, SEQ ID NO:363, SEQ ID NO:364, SEQ ID NO:365,SEQ ID NO:366, SEQ ID NO:2541, SEQ ID NO:2542, SEQ ID NO:2543, SEQ IDNO:2544, SEQ ID NO:2546, SEQ ID NO:2548, SEQ ID NO:2549, SEQ ID NO:2550,SEQ ID NO:2551, SEQ ID NO:2552, and SEQ ID NO:2553.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 14 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:368,SEQ ID NO:369, SEQ ID NO:370, SEQ ID NO:371, SEQ ID NO:372, SEQ IDNO:373, SEQ ID NO:374, SEQ ID NO:376, SEQ ID NO:378, SEQ ID NO:380, SEQID NO:382, SEQ ID NO:384, SEQ ID NO:386, SEQ ID NO:388, SEQ ID NO:390,SEQ ID NO:392, SEQ ID NO:394, SEQ ID NO:396, SEQ ID NO:398, SEQ IDNO:399, SEQ ID NO:401, SEQ ID NO:403, SEQ ID NO:404, SEQ ID NO:406, SEQID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414, SEQ ID NO:416,SEQ ID NO:418, SEQ ID NO:419, SEQ ID NO:420, SEQ ID NO:422, SEQ IDNO:423, SEQ ID NO:425, SEQ ID NO:427, SEQ ID NO:428, SEQ ID NO:430, SEQID NO:432, SEQ ID NO:433, SEQ ID NO:434, SEQ ID NO:435, SEQ ID NO:436,SEQ ID NO:437, SEQ ID NO:438, SEQ ID NO:439, SEQ ID NO:440, SEQ IDNO:441, SEQ ID NO:444, SEQ ID NO:445, SEQ ID NO:446, SEQ ID NO:447, SEQID NO:448, SEQ ID NO:449, SEQ ID NO:450, SEQ ID NO:451, SEQ ID NO:452,SEQ ID NO:453, SEQ ID NO:454, SEQ ID NO:455, SEQ ID NO:456, SEQ IDNO:458, SEQ ID NO:459, SEQ ID NO:461, SEQ ID NO:463, SEQ ID NO:465, SEQID NO:467, SEQ ID NO:469, SEQ ID NO:471, SEQ ID NO:473, SEQ ID NO:474,SEQ ID NO:475, SEQ ID NO:477, SEQ ID NO:479, SEQ ID NO:481, SEQ IDNO:483, SEQ ID NO:485, SEQ ID NO:487, SEQ ID NO:488, SEQ ID NO:489, SEQID NO:490, SEQ ID NO:491, SEQ ID NO:492, SEQ ID NO:494, SEQ ID NO:495,SEQ ID NO:496, SEQ ID NO:497, SEQ ID NO:498, SEQ ID NO:499, SEQ IDNO:500, SEQ ID NO:501, SEQ ID NO:502, SEQ ID NO:504, SEQ ID NO:505, SEQID NO:506, SEQ ID NO:507, and SEQ ID NO:508.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 410 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 15 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:510,SEQ ID NO:511, SEQ ID NO:513, SEQ ID NO:515, SEQ ID NO:517, SEQ IDNO:521, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:527, SEQ ID NO:529, SEQID NO:530, and SEQ ID NO:531.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 520 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 16 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:533,SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:538, SEQ ID NO:539, SEQ IDNO:541, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:544, SEQ ID NO:545, SEQID NO:546, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550, SEQ ID NO:552,SEQ ID NO:553, and SEQ ID NO:554.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 1150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 17 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:558,SEQ ID NO:559, SEQ ID NO:560, SEQ ID NO:561, SEQ ID NO:562, SEQ IDNO:563, SEQ ID NO:564, SEQ ID NO:565, SEQ ID NO:566, SEQ ID NO:567, SEQID NO:569, SEQ ID NO:571, SEQ ID NO:572, SEQ ID NO:573, SEQ ID NO:575,SEQ ID NO:576, SEQ ID NO:577, SEQ ID NO:578, SEQ ID NO:579, SEQ IDNO:581, SEQ ID NO:583, SEQ ID NO:584, SEQ ID NO:585, SEQ ID NO:586, SEQID NO:588, SEQ ID NO:589, SEQ ID NO:590, and SEQ ID NO:591.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 340 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 18 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:593,SEQ ID NO:595, SEQ ID NO:597, SEQ ID NO:599, SEQ ID NO:601, SEQ IDNO:603, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQ ID NO:610, andSEQ ID NO:611.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 140 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 19 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:613,SEQ ID NO:615, SEQ ID NO:617, SEQ ID NO:618, SEQ ID NO:620, SEQ IDNO:622, SEQ ID NO:624, SEQ ID NO:626, SEQ ID NO:628, SEQ ID NO:630, SEQID NO:632, SEQ ID NO:634, SEQ ID NO:636, SEQ ID NO:638, SEQ ID NO:640,SEQ ID NO:642, SEQ ID NO:643, and SEQ ID NO:644.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 250 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 20 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:646,SEQ ID NO:648, SEQ ID NO:650, SEQ ID NO:652, SEQ ID NO:654, SEQ IDNO:656, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:662, SEQ ID NO:664, SEQID NO:666, SEQ ID NO:668, SEQ ID NO:670, SEQ ID NO:672, SEQ ID NO:674,SEQ ID NO:676, SEQ ID NO:678, SEQ ID NO:679, SEQ ID NO:680, SEQ IDNO:681, SEQ ID NO:682, SEQ ID NO:683, and SEQ ID NO:685.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 170 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 21 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:687,SEQ ID NO:689, SEQ ID NO:691, SEQ ID NO:693, SEQ ID NO:694, SEQ IDNO:696, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:701, SEQ ID NO:703, SEQID NO:705, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:710, SEQ ID NO:712,SEQ ID NO:714, SEQ ID NO:716, SEQ ID NO:718, SEQ ID NO:720, SEQ IDNO:721, SEQ ID NO:722, SEQ ID NO:723, SEQ ID NO:724, SEQ ID NO:725, SEQID NO:726, SEQ ID NO:727, and SEQ ID NO:728.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 210 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 22 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:730,SEQ ID NO:732, SEQ ID NO:733, SEQ ID NO:735, SEQ ID NO:737, SEQ IDNO:738, and SEQ ID NO:742.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 230 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 23 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:746,SEQ ID NO:748, SEQ ID NO:750, SEQ ID NO:751, SEQ ID NO:753, SEQ IDNO:755, SEQ ID NO:757, SEQ ID NO:758, SEQ ID NO:760, SEQ ID NO:761, SEQID NO:762, SEQ ID NO:763, SEQ ID NO:765, and SEQ ID NO:767.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 180 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 24 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:769,SEQ ID NO:771, SEQ ID NO:773, SEQ ID NO:775, SEQ ID NO:777, SEQ IDNO:779, SEQ ID NO:781, SEQ ID NO:783, SEQ ID NO:785, SEQ ID NO:787, SEQID NO:789, and SEQ ID NO:790.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 300 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 25 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:792,SEQ ID NO:794, SEQ ID NO:796, SEQ ID NO:798, SEQ ID NO:799, SEQ IDNO:801, SEQ ID NO:803, SEQ ID NO:805, SEQ ID NO:807, SEQ ID NO:808, SEQID NO:810, SEQ ID NO:812, SEQ ID NO:814, SEQ ID NO:816, SEQ ID NO:818,SEQ ID NO:819, SEQ ID NO:820, SEQ ID NO:821, and SEQ ID NO:822.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 190 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 26 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:824,SEQ ID NO:826, SEQ ID NO:1696, SEQ ID NO:1698, SEQ ID NO:1700, SEQ IDNO:1702, SEQ ID NO:1704, SEQ ID NO:1706, SEQ ID NO:1708, SEQ ID NO:1710,SEQ ID NO:1711, SEQ ID NO:1713, SEQ ID NO:1714, SEQ ID NO:1715, and SEQID NO:1716.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 630 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 27 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:828,SEQ ID NO:830, SEQ ID NO:832, SEQ ID NO:834, SEQ ID NO:836, SEQ IDNO:837, SEQ ID NO:838, SEQ ID NO:839, SEQ ID NO:840, SEQ ID NO:842, SEQID NO:844, SEQ ID NO:845, SEQ ID NO:846, SEQ ID NO:847, SEQ ID NO:848,SEQ ID NO:849, SEQ ID NO:850, and SEQ ID NO:851.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 95 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 28 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:855,SEQ ID NO:856, SEQ ID NO:858, SEQ ID NO:860, SEQ ID NO:862, SEQ IDNO:864, SEQ ID NO:866, SEQ ID NO:868, SEQ ID NO:870, SEQ ID NO:872, SEQID NO:874, SEQ ID NO:876, SEQ ID NO:878, SEQ ID NO:880, SEQ ID NO:882,SEQ ID NO:884, SEQ ID NO:885, SEQ ID NO:886, SEQ ID NO:887, SEQ IDNO:888, and SEQ ID NO:889.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 850 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 29 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:891,SEQ ID NO:893, SEQ ID NO:894, SEQ ID NO:895, SEQ ID NO:896, SEQ IDNO:898, SEQ ID NO:900, SEQ ID NO:901, SEQ ID NO:902, SEQ ID NO:903, SEQID NO:904, SEQ ID NO:905, SEQ ID NO:907, SEQ ID NO:908, SEQ ID NO:909,SEQ ID NO:910, SEQ ID NO:911, SEQ ID NO:912, SEQ ID NO:913, SEQ IDNO:914, and SEQ ID NO:915.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 300 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 30 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:917,SEQ ID NO:919, SEQ ID NO:921, SEQ ID NO:923, SEQ ID NO:925, SEQ IDNO:927, SEQ ID NO:929, SEQ ID NO:931, SEQ ID NO:933, SEQ ID NO:935, SEQID NO:937, SEQ ID NO:939, and SEQ ID NO:940.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 60 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 31 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:944,SEQ ID NO:946, SEQ ID NO:947, SEQ ID NO:948, SEQ ID NO:950, SEQ IDNO:952, SEQ ID NO:954, SEQ ID NO:956, SEQ ID NO:958, SEQ ID NO:960, SEQID NO:962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NO:967, SEQ ID NO:968,SEQ ID NO:969, SEQ ID NO:970, SEQ ID NO:972, and SEQ ID NO:974.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 340 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 32 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:976,SEQ ID NO:978, and SEQ ID NO:980.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 180 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 33 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:982,SEQ ID NO:984, SEQ ID NO:985, SEQ ID NO:986, SEQ ID NO:987, SEQ IDNO:988, SEQ ID NO:989, SEQ ID NO:990, SEQ ID NO:991, SEQ ID NO:992, SEQID NO:993, SEQ ID NO:995, SEQ ID NO:996, SEQ ID NO:998, SEQ ID NO:1000,SEQ ID NO:1001, SEQ ID NO:1003, SEQ ID NO:1005, SEQ ID NO:1007, SEQ IDNO:1008, SEQ ID NO:1009, SEQ ID NO:1011, SEQ ID NO:1013, SEQ ID NO:1015,SEQ ID NO:1016, SEQ ID NO:1018, SEQ ID NO:1019, SEQ ID NO:1021, SEQ IDNO:1023, SEQ ID NO:1025, SEQ ID NO:1026, SEQ ID NO:1027, SEQ ID NO:1028,SEQ ID NO:1029, SEQ ID NO:1030, SEQ ID NO:1031, SEQ ID NO:1032, and SEQID NO:1033.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 1060 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 34 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1054,SEQ ID NO:1055, SEQ ID NO:1057, SEQ ID NO:1058, SEQ ID NO:1059, SEQ IDNO:1061, SEQ ID NO:1063, SEQ ID NO:1065, SEQ ID NO:1065, SEQ ID NO:1067,SEQ ID NO:1068, SEQ ID NO:1070, SEQ ID NO:1071, SEQ ID NO:1072, SEQ IDNO:1074, SEQ ID NO:1075, SEQ ID NO:1076, SEQ ID NO:1077, SEQ ID NO:1078,SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1083, SEQ ID NO:1085, SEQ IDNO:1086, SEQ ID NO:1087, SEQ ID NO:1088, SEQ ID NO:1089, SEQ ID NO:1089,SEQ ID NO:1090, SEQ ID NO:1091, SEQ ID NO:1092, SEQ ID NO:1093, SEQ IDNO:1094, SEQ ID NO:1095, and SEQ ID NO:1097.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 260 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 35 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1099,SEQ ID NO:1101, SEQ ID NO:1103, SEQ ID NO:1104, SEQ ID NO:1105, SEQ IDNO:1106, SEQ ID NO:1108, SEQ ID NO:1109, and SEQ ID NO:1110.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 36 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1112,SEQ ID NO:1113, and SEQ ID NO:1114.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 40 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 37 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1116,SEQ ID NO:1118, SEQ ID NO:1120, SEQ ID NO:1122, SEQ ID NO:1123, SEQ IDNO:1125, SEQ ID NO:1126, SEQ ID NO:1128, SEQ ID NO:1129, SEQ ID NO:1131,SEQ ID NO:1132, SEQ ID NO:1133, SEQ ID NO:1134, SEQ ID NO:1136, SEQ IDNO:1138, SEQ ID NO:1140, SEQ ID NO:1141, SEQ ID NO:1142, SEQ ID NO:1143,SEQ ID NO:1144, SEQ ID NO:1145, SEQ ID NO:1147, SEQ ID NO:1149, SEQ IDNO:1151, SEQ ID NO:1153, and SEQ ID NO:1155.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 450 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 38 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1159,SEQ ID NO:1161, SEQ ID NO:1162, SEQ ID NO:1163, and SEQ ID NO:1164.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 160 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 39 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1166,SEQ ID NO:1167, SEQ ID NO:1169, SEQ ID NO:1171, SEQ ID NO:1173, SEQ IDNO:1175, SEQ ID NO:1177, SEQ ID NO:1179, SEQ ID NO:1180, SEQ ID NO:1182,and SEQ ID NO:1183.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 180 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 40 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1185,SEQ ID NO:1187, SEQ ID NO:1189, SEQ ID NO:1190, SEQ ID NO:1191, and SEQID NO:1192.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 670 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 41 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1194,SEQ ID NO:1196, SEQ ID NO:1198, SEQ ID NO:1200, SEQ ID NO:1202, SEQ IDNO:1203, SEQ ID NO:1204, SEQ ID NO:1205, SEQ ID NO:1206, SEQ ID NO:1207,and SEQ ID NO:1208.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 280 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 42 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1210,SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQ ID NO:1216, SEQ IDNO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ ID NO:1224, SEQ ID NO:1226,SEQ ID NO:1228, SEQ ID NO:1229, SEQ ID NO:1230, SEQ ID NO:1232, SEQ IDNO:1233, SEQ ID NO:1234, SEQ ID NO:1235, SEQ ID NO:1236, SEQ ID NO:1237,SEQ ID NO:1238, SEQ ID NO:1239, SEQ ID NO:1240, SEQ ID NO:1241, SEQ IDNO:1242, SEQ ID NO:1243, SEQ ID NO:1244, SEQ ID NO:1245, SEQ ID NO:1246,SEQ ID NO:1247, SEQ ID NO:1248, SEQ ID NO:1249, SEQ ID NO:1251, SEQ IDNO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ ID NO:1259, SEQ ID NO:1261,SEQ ID NO:1263, SEQ ID NO:1264, SEQ ID NO:1265, SEQ ID NO:1266, SEQ IDNO:1267, SEQ ID NO:1268, SEQ ID NO:1269, SEQ ID NO:1270, SEQ ID NO:1271,and SEQ ID NO:1272.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 700 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 43 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1274,SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQ ID NO:1281, SEQ IDNO:1282, SEQ ID NO:1284, SEQ ID NO:1285, SEQ ID NO:1287, SEQ ID NO:1289,SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1294, SEQ ID NO:1295, SEQ IDNO:1296, SEQ ID NO:1297, SEQ ID NO:1298, and SEQ ID NO:1300.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 920 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 44 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1302,SEQ ID NO:1303, SEQ ID NO:1305, SEQ ID NO:1307, SEQ ID NO:1309, SEQ IDNO:1311, SEQ ID NO:1312, SEQ ID NO:1313, SEQ ID NO:1314, SEQ ID NO:1315,SEQ ID NO:1317, SEQ ID NO:1318, SEQ ID NO:1319, SEQ ID NO:1320, SEQ IDNO:1321, SEQ ID NO:1322, SEQ ID NO:1323, SEQ ID NO:1324, SEQ ID NO:1325,SEQ ID NO:1326, SEQ ID NO:1327, SEQ ID NO:1328, SEQ ID NO:1330, SEQ IDNO:1331, SEQ ID NO:1333, SEQ ID NO:1334, SEQ ID NO:1335, SEQ ID NO:1336,SEQ ID NO:1337, SEQ ID NO:1338, SEQ ID NO:1339, and SEQ ID NO:1340.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 510 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 45 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1342,SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQ ID NO:1350, SEQ IDNO:1352, SEQ ID NO:1354, SEQ ID NO:1355, SEQ ID NO:1357, SEQ ID NO:1358,SEQ ID NO:1360, SEQ ID NO:1361, SEQ ID NO:1362, SEQ ID NO:1363, SEQ IDNO:1364, SEQ ID NO:1366, SEQ ID NO:1367, SEQ ID NO:1369, SEQ ID NO:1370,SEQ ID NO:1371, SEQ ID NO:1372, SEQ ID NO:1373, SEQ ID NO:1374, SEQ IDNO:1375, SEQ ID NO:1376, SEQ ID NO:1377, SEQ ID NO:1378, SEQ ID NO:1379,SEQ ID NO:1380, SEQ ID NO:1381, SEQ ID NO:1382, and SEQ ID NO:1383.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 140 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 46 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1385,SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1390, SEQ ID NO:1391, SEQ IDNO:1393, SEQ ID NO:1394, SEQ ID NO:1395, SEQ ID NO:1396, SEQ ID NO:1398,SEQ ID NO:1400, SEQ ID NO:1401, SEQ ID NO:1402, SEQ ID NO:1403, SEQ IDNO:1404, SEQ ID NO:1405, and SEQ ID NO:1407.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 150 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 47 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1409,SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1415, SEQ ID NO:1417, SEQ IDNO:1418, SEQ ID NO:1419, SEQ ID NO:1421, SEQ ID NO:1423, SEQ ID NO:1424,SEQ ID NO:1425, SEQ ID NO:1426.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 190 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 48 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1428,SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQ ID NO:1436, SEQ IDNO:1439, SEQ ID NO:1442, SEQ ID NO:1444, SEQ ID NO:1446, SEQ ID NO:1448,SEQ ID NO:1450, SEQ ID NO:1452, SEQ ID NO:1453, SEQ ID NO:1454, SEQ IDNO:1455, SEQ ID NO:1456, SEQ ID NO:1457, SEQ ID NO:1458, and SEQ IDNO:1459.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 450 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 49 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1463,SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQ ID NO:1471, SEQ IDNO:1473, SEQ ID NO:1474, SEQ ID NO:1475, SEQ ID NO:1476, and SEQ IDNO:1477.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 580 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 50 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1491,SEQ ID NO:1493, SEQ ID NO:1495, SEQ ID NO:1497, SEQ ID NO:1499, SEQ IDNO:1501, SEQ ID NO:1503, SEQ ID NO:1504, SEQ ID NO:1505, SEQ ID NO:1506,and SEQ ID NO:1508.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 100 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 51 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1510,SEQ ID NO:1512, SEQ ID NO:1514, SEQ ID NO:1516, SEQ ID NO:1518, SEQ IDNO:1520, SEQ ID NO:1522, and SEQ ID NO:1523.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 800 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 52 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1525,SEQ ID NO:1527, SEQ ID NO:1529, SEQ ID NO:1530, SEQ ID NO:1532, SEQ IDNO:1534, and SEQ ID NO:1535.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 490 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 53 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1537,SEQ ID NO:1539, SEQ ID NO:1540, SEQ ID NO:1541, SEQ ID NO:1543, SEQ IDNO:1545, SEQ ID NO:1547, SEQ ID NO:1548, SEQ ID NO:1550, SEQ ID NO:1552,SEQ ID NO:2386, SEQ ID NO:2388, SEQ ID NO:2390, SEQ ID NO:2391, and SEQID NO:2392.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 690 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 54 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1554,SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQ ID NO:1561, SEQ IDNO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ ID NO:1569, SEQ ID NO:1571,SEQ ID NO:1572, SEQ ID NO:1573, SEQ ID NO:1574, and SEQ ID NO:1575.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 380 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 55 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:1035,SEQ ID NO:1036, SEQ ID NO:1037, SEQ ID NO:1040, SEQ ID NO:1041, SEQ IDNO:1043, SEQ ID NO:1044, SEQ ID NO:1046, SEQ ID NO:1047, SEQ ID NO:1048,SEQ ID NO:1050, SEQ ID NO:1440, SEQ ID NO:1480, SEQ ID NO:1481, SEQ IDNO:1482, SEQ ID NO:1483, SEQ ID NO:1484, SEQ ID NO:1485, SEQ ID NO:1486,SEQ ID NO:1487, SEQ ID NO:1488, SEQ ID NO:1577, SEQ ID NO:1578, SEQ IDNO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ ID NO:1586, SEQ ID NO:1588,SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594, SEQ ID NO:1596, SEQ IDNO:1598, SEQ ID NO:1599, SEQ ID NO:1601, SEQ ID NO:1602, SEQ ID NO:1605,SEQ ID NO:1607, SEQ ID NO:1608, SEQ ID NO:1609, SEQ ID NO:1611, SEQ IDNO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ ID NO:1619, SEQ ID NO:1621,SEQ ID NO:1622, SEQ ID NO:1623, SEQ ID NO:1624, SEQ ID NO:1625, SEQ IDNO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ ID NO:1633, SEQ ID NO:1635,SEQ ID NO:1637, SEQ ID NO:1639, SEQ ID NO:1643, SEQ ID NO:1645, SEQ IDNO:1648, SEQ ID NO:1649, SEQ ID NO:1651, and SEQ ID NO:1653.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 870 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 56 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:173,SEQ ID NO:212, SEQ ID NO:361, SEQ ID NO:421, SEQ ID NO:443, SEQ IDNO:740, SEQ ID NO:744, SEQ ID NO:942, SEQ ID NO:1437, and SEQ IDNO:1461.

Examples of polypeptides are shown in the sequence listing that have HMMbit scores greater than 140 when fitted to an HMM generated from theamino acid sequences set forth in FIG. 57 are identified in the SequenceListing of this application. Such polypeptides include SEQ ID NO:97, SEQID NO:2010, SEQ ID NO:2011, SEQ ID NO:2013, SEQ ID NO:2015, and SEQ IDNO:2017.

D. Percent Identity

In some embodiments, a low nitrogen tolerance-modulating polypeptide hasan amino acid sequence with at least 20% sequence identity, e.g., atleast 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%,98%, or 99% sequence identity, to one of the amino acid sequences setforth in SEQ ID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ IDNO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332,SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ IDNO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824,SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ IDNO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ IDNO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210,SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ IDNO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491,SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQID NO:1577. Polypeptides having such a percent sequence identity oftenhave a domain indicative of a low nitrogen tolerance-modulatingpolypeptide and/or have an HMM bit score that is greater than 20, asdiscussed above. Amino acid sequences of low nitrogentolerance-modulating polypeptides having at least 20% sequence identityto one of the amino acid sequences set forth in SEQ ID NO:3, SEQ IDNO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ IDNO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510,SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ IDNO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853,SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ IDNO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112,SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ IDNO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302,SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ IDNO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525,SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577 are provided in FIGS.1-57 and in the Sequence Listing.

“Percent sequence identity” refers to the degree of sequence identitybetween any given reference sequence, e.g., SEQ ID NO:3, and a candidatelow nitrogen tolerance-modulating sequence. A candidate sequencetypically has a length that is from 80 percent to 200 percent of thelength of the reference sequence, e.g., 82, 85, 87, 89, 90, 93, 95, 97,99, 100, 105, 110, 115, 120, 130, 140, 150, 160, 170, 180, 190, or 200percent of the length of the reference sequence. A percent identity forany candidate nucleic acid or polypeptide relative to a referencenucleic acid or polypeptide can be determined as follows. A referencesequence (e.g., a nucleic acid sequence or an amino acid sequence) isaligned to one or more candidate sequences using the computer programClustalW (version 1.83, default parameters), which allows alignments ofnucleic acid or polypeptide sequences to be carried out across theirentire length (global alignment). Chenna et al. (2003) Nucleic AcidsRes., 31(13):3497-500.

ClustalW calculates the best match between a reference and one or morecandidate sequences, and aligns them so that identities, similaritiesand differences can be determined. Gaps of one or more residues can beinserted into a reference sequence, a candidate sequence, or both, tomaximize sequence alignments. For fast pairwise alignment of nucleicacid sequences, the following default parameters are used: word size: 2;window size: 4; scoring method: percentage; number of top diagonals: 4;and gap penalty: 5. For multiple alignment of nucleic acid sequences,the following parameters are used: gap opening penalty: 10.0; gapextension penalty: 5.0; and weight transitions: yes. For fast pairwisealignment of protein sequences, the following parameters are used: wordsize: 1; window size: 5; scoring method: percentage; number of topdiagonals: 5; gap penalty: 3. For multiple alignment of proteinsequences, the following parameters are used: weight matrix: blosum; gapopening penalty: 10.0; gap extension penalty: 0.05; hydrophilic gaps:on; hydrophilic residues: Gly, Pro, Ser, Asn, Asp, Gln, Glu, Arg, andLys; residue-specific gap penalties: on. The ClustalW output is asequence alignment that reflects the relationship between sequences.ClustalW can be run, for example, at the Baylor College of MedicineSearch Launcher site(searchlauncher.bcm.tmc.edu/multi-align/multi-align.html) and at theEuropean Bioinformatics Institute site on the World Wide Web(ebi.ac.uk/clustalw).

To determine percent identity of a candidate nucleic acid or amino acidsequence to a reference sequence, the sequences are aligned usingClustalW, the number of identical matches in the alignment is divided bythe length of the reference sequence, and the result is multiplied by100. It is noted that the percent identity value can be rounded to thenearest tenth. For example, 78.11, 78.12, 78.13, and 78.14 are roundeddown to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 are rounded upto 78.2.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:3, and preferably has at least 20% sequenceidentity, e.g., 50%, 52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 97%, 98%, or 99% sequence identity, to the amino acid sequence setforth in SEQ ID NO:3. Amino acid sequences of polypeptides havinggreater than 20% sequence identity to the polypeptide set forth in SEQID NO:3 are provided in FIG. 1 and in the Sequence Listing. Examples ofsuch polypeptides include SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ IDNO:10, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ IDNO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:24, SEQ IDNO:25, SEQ ID NO:27, SEQ ID NO:29, SEQ ID NO:31, SEQ ID NO:33, SEQ IDNO:35, SEQ ID NO:36, SEQ ID NO:38, SEQ ID NO:39, SEQ ID NO:40, SEQ IDNO:41, SEQ ID NO:42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO:45, SEQ IDNO:46, and SEQ ID NO:47.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:49, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:49.Amino acid sequences of polypeptides having greater than 45% sequenceidentity to the polypeptide set forth in SEQ ID NO:49 are provided inFIG. 2 and in the Sequence Listing. Examples of such polypeptidesinclude SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:56, SEQ IDNO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:63, SEQ ID NO:64, SEQ IDNO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ IDNO:72, SEQ ID NO:73, and SEQ ID NO:75.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:77, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:77.Amino acid sequences of polypeptides having greater than 45% sequenceidentity to the polypeptide set forth in SEQ ID NO:77 are provided inFIG. 3 and in the Sequence Listing. Examples of such polypeptidesinclude SEQ ID NO:78, SEQ ID NO:80, SEQ ID NO:82, SEQ ID NO:84, SEQ IDNO:85, SEQ ID NO:87, SEQ ID NO:88, SEQ ID NO:90, SEQ ID NO:92, SEQ IDNO:93, SEQ ID NO:95, SEQ ID NO:1479.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:100, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:100. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO: 100 areprovided in FIG. 4 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:101, SEQ ID NO:102, SEQ ID NO:104, SEQ IDNO:106, SEQ ID NO:108, SEQ ID NO:110, SEQ ID NO:111, SEQ ID NO:113, SEQID NO:115, SEQ ID NO:116, SEQ ID NO:117, SEQ ID NO:118, SEQ ID NO:119,SEQ ID NO:120, SEQ ID NO:121, SEQ ID NO:122, SEQ ID NO:123, SEQ IDNO:125, SEQ ID NO:126, SEQ ID NO:128, SEQ ID NO:129, SEQ ID NO:130, SEQID NO:131, SEQ ID NO:132, SEQ ID NO:133, SEQ ID NO:134, SEQ ID NO:135,SEQ ID NO:137, SEQ ID NO:139, SEQ ID NO:141, SEQ ID NO:142, SEQ IDNO:144, SEQ ID NO:145, SEQ ID NO:146, SEQ ID NO:147, SEQ ID NO:148, SEQID NO:149, and SEQ ID NO:150.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:152, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:152. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:152 areprovided in FIG. 5 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:154, SEQ ID NO:156, SEQ ID NO:158, SEQ IDNO:160, SEQ ID NO:162, and SEQ ID NO:164.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:166, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:166. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:166 areprovided in FIG. 6 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:166, SEQ ID NO:168, SEQ ID NO:170, SEQ IDNO:172, SEQ ID NO:174, SEQ ID NO:177, SEQ ID NO:179, SEQ ID NO:181, SEQID NO:182, SEQ ID NO:183, SEQ ID NO:184.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:186, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:186. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:186 areprovided in FIG. 7 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:188, SEQ ID NO:190, SEQ ID NO:191, SEQ IDNO:193, SEQ ID NO:194, SEQ ID NO:196, SEQ ID NO:197, SEQ ID NO:199, SEQID NO:201, SEQ ID NO:203, SEQ ID NO:204, SEQ ID NO:205, and SEQ IDNO:206.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:208, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:208. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:208 areprovided in FIG. 8 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:209, SEQ ID NO:210, SEQ ID NO:214, andSEQ ID NO:216.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:218, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:218. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:218 areprovided in FIG. 9 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:218, SEQ ID NO:220, SEQ ID NO:222, SEQ IDNO:223, SEQ ID NO:225, SEQ ID NO:227, SEQ ID NO:229, SEQ ID NO:230, SEQID NO:231, SEQ ID NO:232, SEQ ID NO:1039, SEQ ID NO:1049, and SEQ IDNO:1052.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:234, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:234. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:234 areprovided in FIG. 10 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:236, SEQ ID NO:238, SEQ ID NO:239, SEQ IDNO:241, SEQ ID NO:242, SEQ ID NO:243, and SEQ ID NO:244.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:246, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:246. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:246 areprovided in FIG. 11 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:248, SEQ ID NO:249, SEQ ID NO:251, SEQ IDNO:253, SEQ ID NO:255, SEQ ID NO:257, SEQ ID NO:259, SEQ ID NO:260, SEQID NO:262, SEQ ID NO:264, SEQ ID NO:265, SEQ ID NO:267, SEQ ID NO:268,SEQ ID NO:270, SEQ ID NO:272, SEQ ID NO:274, SEQ ID NO:276, SEQ IDNO:277, SEQ ID NO:279, SEQ ID NO:281, SEQ ID NO:283, SEQ ID NO:285, SEQID NO:286, SEQ ID NO:287, SEQ ID NO:288, SEQ ID NO:290, SEQ ID NO:291,SEQ ID NO:292, SEQ ID NO:293, SEQ ID NO:296, and SEQ ID NO:298.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:300, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:300. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:300 areprovided in FIG. 12 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:302, SEQ ID NO:304, SEQ ID NO:306, SEQ IDNO:308, SEQ ID NO:310, SEQ ID NO:312, SEQ ID NO:314, SEQ ID NO:316, SEQID NO:318, SEQ ID NO:319, SEQ ID NO:320, SEQ ID NO:321, SEQ ID NO:322,SEQ ID NO:323, SEQ ID NO:325, SEQ ID NO:327, and SEQ ID NO:329.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:332, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:332. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:332 areprovided in FIG. 13 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:332, SEQ ID NO:334, SEQ ID NO:335, SEQ IDNO:336, SEQ ID NO:338, SEQ ID NO:339, SEQ ID NO:341, SEQ ID NO:342, SEQID NO:343, SEQ ID NO:344, SEQ ID NO:345, SEQ ID NO:346, SEQ ID NO:347,SEQ ID NO:348, SEQ ID NO:349, SEQ ID NO:351, SEQ ID NO:352, SEQ IDNO:353, SEQ ID NO:354, SEQ ID NO:355, SEQ ID NO:356, SEQ ID NO:357, SEQID NO:358, SEQ ID NO:359, SEQ ID NO:360, SEQ ID NO:362, SEQ ID NO:363,SEQ ID NO:364, SEQ ID NO:365, SEQ ID NO:366, SEQ ID NO:2541, SEQ IDNO:2542, SEQ ID NO:2543, SEQ ID NO:2544, SEQ ID NO:2546, SEQ ID NO:2548,SEQ ID NO:2549, SEQ ID NO:2550, SEQ ID NO:2551, SEQ ID NO:2552, and SEQID NO:2553.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:368, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:368. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:368 areprovided in FIG. 14 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:369, SEQ ID NO:370, SEQ ID NO:371, SEQ IDNO:372, SEQ ID NO:373, SEQ ID NO:374, SEQ ID NO:376, SEQ ID NO:378, SEQID NO:380, SEQ ID NO:382, SEQ ID NO:384, SEQ ID NO:386, SEQ ID NO:388,SEQ ID NO:390, SEQ ID NO:392, SEQ ID NO:394, SEQ ID NO:396, SEQ IDNO:398, SEQ ID NO:399, SEQ ID NO:401, SEQ ID NO:403, SEQ ID NO:404, SEQID NO:406, SEQ ID NO:408, SEQ ID NO:410, SEQ ID NO:412, SEQ ID NO:414,SEQ ID NO:416, SEQ ID NO:418, SEQ ID NO:419, SEQ ID NO:420, SEQ IDNO:422, SEQ ID NO:423, SEQ ID NO:425, SEQ ID NO:427, SEQ ID NO:428, SEQID NO:430, SEQ ID NO:432, SEQ ID NO:433, SEQ ID NO:434, SEQ ID NO:435,SEQ ID NO:436, SEQ ID NO:437, SEQ ID NO:438, SEQ ID NO:439, SEQ IDNO:440, SEQ ID NO:441, SEQ ID NO:444, SEQ ID NO:445, SEQ ID NO:446, SEQID NO:447, SEQ ID NO:448, SEQ ID NO:449, SEQ ID NO:450, SEQ ID NO:451,SEQ ID NO:452, SEQ ID NO:453, SEQ ID NO:454, SEQ ID NO:455, SEQ IDNO:456, SEQ ID NO:458, SEQ ID NO:459, SEQ ID NO:461, SEQ ID NO:463, SEQID NO:465, SEQ ID NO:467, SEQ ID NO:469, SEQ ID NO:471, SEQ ID NO:473,SEQ ID NO:474, SEQ ID NO:475, SEQ ID NO:477, SEQ ID NO:479, SEQ IDNO:481, SEQ ID NO:483, SEQ ID NO:485, SEQ ID NO:487, SEQ ID NO:488, SEQID NO:489, SEQ ID NO:490, SEQ ID NO:491, SEQ ID NO:492, SEQ ID NO:494,SEQ ID NO:495, SEQ ID NO:496, SEQ ID NO:497, SEQ ID NO:498, SEQ IDNO:499, SEQ ID NO:500, SEQ ID NO:501, SEQ ID NO:502, SEQ ID NO:504, SEQID NO:505, SEQ ID NO:506, SEQ ID NO:507, and SEQ ID NO:508.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:510, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:510. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:510 areprovided in FIG. 15 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:511, SEQ ID NO:513, SEQ ID NO:515, SEQ IDNO:517, SEQ ID NO:521, SEQ ID NO:523, SEQ ID NO:525, SEQ ID NO:527, SEQID NO:529, SEQ ID NO:530, and SEQ ID NO:531.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:533, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:533. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:533 areprovided in FIG. 16 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:535, SEQ ID NO:536, SEQ ID NO:538, SEQ IDNO:539, SEQ ID NO:541, SEQ ID NO:542, SEQ ID NO:543, SEQ ID NO:544, SEQID NO:545, SEQ ID NO:546, SEQ ID NO:547, SEQ ID NO:548, SEQ ID NO:550,SEQ ID NO:552, SEQ ID NO:553, and SEQ ID NO:554.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:558, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:558. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:558 areprovided in FIG. 17 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:559, SEQ ID NO:560, SEQ ID NO:561, SEQ IDNO:562, SEQ ID NO:563, SEQ ID NO:564, SEQ ID NO:565, SEQ ID NO:566, SEQID NO:567, SEQ ID NO:569, SEQ ID NO:571, SEQ ID NO:572, SEQ ID NO:573,SEQ ID NO:575, SEQ ID NO:576, SEQ ID NO:577, SEQ ID NO:578, SEQ IDNO:579, SEQ ID NO:581, SEQ ID NO:583, SEQ ID NO:584, SEQ ID NO:585, SEQID NO:586, SEQ ID NO:588, SEQ ID NO:589, SEQ ID NO:590, and SEQ IDNO:591.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:593, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:593. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:593 areprovided in FIG. 18 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:595, SEQ ID NO:597, SEQ ID NO:599, SEQ IDNO:601, SEQ ID NO:603, SEQ ID NO:605, SEQ ID NO:607, SEQ ID NO:609, SEQID NO:610, and SEQ ID NO:611.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:613, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:613. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:613 areprovided in FIG. 19 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:615, SEQ ID NO:617, SEQ ID NO:618, SEQ IDNO:620, SEQ ID NO:622, SEQ ID NO:624, SEQ ID NO:626, SEQ ID NO:628, SEQID NO:630, SEQ ID NO:632, SEQ ID NO:634, SEQ ID NO:636, SEQ ID NO:638,SEQ ID NO:640, SEQ ID NO:642, SEQ ID NO:643, and SEQ ID NO:644.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:646, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:646. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:646 areprovided in FIG. 20 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:648, SEQ ID NO:650, SEQ ID NO:652, SEQ IDNO:654, SEQ ID NO:656, SEQ ID NO:658, SEQ ID NO:660, SEQ ID NO:662, SEQID NO:664, SEQ ID NO:666, SEQ ID NO:668, SEQ ID NO:670, SEQ ID NO:672,SEQ ID NO:674, SEQ ID NO:676, SEQ ID NO:678, SEQ ID NO:679, SEQ IDNO:680, SEQ ID NO:681, SEQ ID NO:682, SEQ ID NO:683, and SEQ ID NO:685.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:687, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:687. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:687 areprovided in FIG. 21 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:689, SEQ ID NO:691, SEQ ID NO:693, SEQ IDNO:694, SEQ ID NO:696, SEQ ID NO:697, SEQ ID NO:699, SEQ ID NO:701, SEQID NO:703, SEQ ID NO:705, SEQ ID NO:706, SEQ ID NO:708, SEQ ID NO:710,SEQ ID NO:712, SEQ ID NO:714, SEQ ID NO:716, SEQ ID NO:718, SEQ IDNO:720, SEQ ID NO:721, SEQ ID NO:722, SEQ ID NO:723, SEQ ID NO:724, SEQID NO:725, SEQ ID NO:726, SEQ ID NO:727, and SEQ ID NO:728.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:730, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:730. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:730 areprovided in FIG. 22 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:732, SEQ ID NO:733, SEQ ID NO:735, SEQ IDNO:737, SEQ ID NO:738, and SEQ ID NO:742.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:746, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:746. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:746 areprovided in FIG. 23 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:748, SEQ ID NO:750, SEQ ID NO:751, SEQ IDNO:753, SEQ ID NO:755, SEQ ID NO:757, SEQ ID NO:758, SEQ ID NO:760, SEQID NO:761, SEQ ID NO:762, SEQ ID NO:763, SEQ ID NO:765, and SEQ IDNO:767.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:769, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:769. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:769 areprovided in FIG. 24 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:771, SEQ ID NO:773, SEQ ID NO:775, SEQ IDNO:777, SEQ ID NO:779, SEQ ID NO:781, SEQ ID NO:783, SEQ ID NO:785, SEQID NO:787, SEQ ID NO:789, and SEQ ID NO:790.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:792, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:792. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:792 areprovided in FIG. 25 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:794, SEQ ID NO:796, SEQ ID NO:798, SEQ IDNO:799, SEQ ID NO:801, SEQ ID NO:803, SEQ ID NO:805, SEQ ID NO:807, SEQID NO:808, SEQ ID NO:810, SEQ ID NO:812, SEQ ID NO:814, SEQ ID NO:816,SEQ ID NO:818, SEQ ID NO:819, SEQ ID NO:820, SEQ ID NO:821, and SEQ IDNO:822.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:824, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:824. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:824 areprovided in FIG. 26 and in the Sequence Listing. Such polypeptidesinclude, but not limited to, SEQ ID NO:826, SEQ ID NO:1696, SEQ IDNO:1698, SEQ ID NO:1700, SEQ ID NO:1702, SEQ ID NO:1704, SEQ ID NO:1706,SEQ ID NO:1708, SEQ ID NO:1710, SEQ ID NO:1711, SEQ ID NO:1713, SEQ IDNO:1714, SEQ ID NO:1715, and SEQ ID NO:1716.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:828, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:828. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:828 areprovided in FIG. 27 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:830, SEQ ID NO:832, SEQ ID NO:834, SEQ IDNO:836, SEQ ID NO:837, SEQ ID NO:838, SEQ ID NO:839, SEQ ID NO:840, SEQID NO:842, SEQ ID NO:844, SEQ ID NO:845, SEQ ID NO:846, SEQ ID NO:847,SEQ ID NO:848, SEQ ID NO:849, SEQ ID NO:850, and SEQ ID NO:851.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:855, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:855. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:855 areprovided in FIG. 28 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:856, SEQ ID NO:858, SEQ ID NO:860, SEQ IDNO:862, SEQ ID NO:864, SEQ ID NO:866, SEQ ID NO:868, SEQ ID NO:870, SEQID NO:872, SEQ ID NO:874, SEQ ID NO:876, SEQ ID NO:878, SEQ ID NO:880,SEQ ID NO:882, SEQ ID NO:884, SEQ ID NO:885, SEQ ID NO:886, SEQ IDNO:887, SEQ ID NO:888, and SEQ ID NO:889.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:891, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:891. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:891 areprovided in FIG. 29 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:893, SEQ ID NO:894, SEQ ID NO:895, SEQ IDNO:896, SEQ ID NO:898, SEQ ID NO:900, SEQ ID NO:901, SEQ ID NO:902, SEQID NO:903, SEQ ID NO:904, SEQ ID NO:905, SEQ ID NO:907, SEQ ID NO:908,SEQ ID NO:909, SEQ ID NO:910, SEQ ID NO:911, SEQ ID NO:912, SEQ IDNO:913, SEQ ID NO:914, and SEQ ID NO:915.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:917, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:917. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:917 areprovided in FIG. 30 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:919, SEQ ID NO:921, SEQ ID NO:923, SEQ IDNO:925, SEQ ID NO:927, SEQ ID NO:929, SEQ ID NO:931, SEQ ID NO:933, SEQID NO:935, SEQ ID NO:937, SEQ ID NO:939, and SEQ ID NO:940.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:944, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:944. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:944 areprovided in FIG. 31 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:946, SEQ ID NO:947, SEQ ID NO:948, SEQ IDNO:950, SEQ ID NO:952, SEQ ID NO:954, SEQ ID NO:956, SEQ ID NO:958, SEQID NO:960, SEQ ID NO:962, SEQ ID NO:964, SEQ ID NO:966, SEQ ID NO:967,SEQ ID NO:968, SEQ ID NO:969, SEQ ID NO:970, SEQ ID NO:972, and SEQ IDNO:974.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:976, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:976. Amino acid sequences of polypeptides having greater than 45%sequence identity to the polypeptide set forth in SEQ ID NO:976 areprovided in FIG. 32 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:978 and SEQ ID NO:980.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:982, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:982. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:982 areprovided in FIG. 33 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:984, SEQ ID NO:985, SEQ ID NO:986, SEQ IDNO:987, SEQ ID NO:988, SEQ ID NO:989, SEQ ID NO:990, SEQ ID NO:991, SEQID NO:992, SEQ ID NO:993, SEQ ID NO:995, SEQ ID NO:996, SEQ ID NO:998,SEQ ID NO:1000, SEQ ID NO:1001, SEQ ID NO:1003, SEQ ID NO:1005, SEQ IDNO:1007, SEQ ID NO:1008, SEQ ID NO:1009, SEQ ID NO:1011, SEQ ID NO:1013,SEQ ID NO:1015, SEQ ID NO:1016, SEQ ID NO:1018, SEQ ID NO:1019, SEQ IDNO:1021, SEQ ID NO:1023, SEQ ID NO:1025, SEQ ID NO:1026, SEQ ID NO:1027,SEQ ID NO:1028, SEQ ID NO:1029, SEQ ID NO:1030, SEQ ID NO:1031, SEQ IDNO:1032, and SEQ ID NO:1033.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1054, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1054. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1054 areprovided in FIG. 34 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1055, SEQ ID NO:1057, SEQ ID NO:1058, SEQID NO:1059, SEQ ID NO:1061, SEQ ID NO:1063, SEQ ID NO:1065, SEQ IDNO:1065, SEQ ID NO:1067, SEQ ID NO:1068, SEQ ID NO:1070, SEQ ID NO:1071,SEQ ID NO:1072, SEQ ID NO:1074, SEQ ID NO:1075, SEQ ID NO:1076, SEQ IDNO:1077, SEQ ID NO:1078, SEQ ID NO:1080, SEQ ID NO:1082, SEQ ID NO:1083,SEQ ID NO:1085, SEQ ID NO:1086, SEQ ID NO:1087, SEQ ID NO:1088, SEQ IDNO:1089, SEQ ID NO:1089, SEQ ID NO:1090, SEQ ID NO:1091, SEQ ID NO:1092,SEQ ID NO:1093, SEQ ID NO:1094, SEQ ID NO:1095, and SEQ ID NO:1097.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1099, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1099. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1099 areprovided in FIG. 35 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1101, SEQ ID NO:1103, SEQ ID NO:1104, SEQID NO:1105, SEQ ID NO:1106, SEQ ID NO:1108, SEQ ID NO:1109, and SEQ IDNO:1110.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1112, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1112. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1112 areprovided in FIG. 36 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1113 and SEQ ID NO:1114.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1116, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1116. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1116 areprovided in FIG. 37 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1118, SEQ ID NO:1120, SEQ ID NO:1122, SEQID NO:1123, SEQ ID NO:1125, SEQ ID NO:1126, SEQ ID NO:1128, SEQ IDNO:1129, SEQ ID NO:1131, SEQ ID NO:1132, SEQ ID NO:1133, SEQ ID NO:1134,SEQ ID NO:1136, SEQ ID NO:1138, SEQ ID NO:1140, SEQ ID NO:1141, SEQ IDNO:1142, SEQ ID NO:1143, SEQ ID NO:1144, SEQ ID NO:1145, SEQ ID NO:1147,SEQ ID NO:1149, SEQ ID NO:1151, SEQ ID NO:1153, and SEQ ID NO:1155.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1159, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1159. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1159 areprovided in FIG. 38 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1161, SEQ ID NO:1162, SEQ ID NO:1163, andSEQ ID NO:1164.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1166, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1166. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1166 areprovided in FIG. 39 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1167, SEQ ID NO:1169, SEQ ID NO:1171, SEQID NO:1173, SEQ ID NO:1175, SEQ ID NO:1177, SEQ ID NO:1179, SEQ IDNO:1180, SEQ ID NO:1182, and SEQ ID NO:1183.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1185, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1185. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1185 areprovided in FIG. 40 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1187, SEQ ID NO:1189, SEQ ID NO:1190, SEQID NO:1191, and SEQ ID NO:1192.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1194, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1194. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1194 areprovided in FIG. 41 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1196, SEQ ID NO:1198, SEQ ID NO:1200, SEQID NO:1202, SEQ ID NO:1203, SEQ ID NO:1204, SEQ ID NO:1205, SEQ IDNO:1206, SEQ ID NO:1207, and SEQ ID NO:1208.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1210, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1210. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1210 areprovided in FIG. 42 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1211, SEQ ID NO:1213, SEQ ID NO:1215, SEQID NO:1216, SEQ ID NO:1218, SEQ ID NO:1220, SEQ ID NO:1222, SEQ IDNO:1224, SEQ ID NO:1226, SEQ ID NO:1228, SEQ ID NO:1229, SEQ ID NO:1230,SEQ ID NO:1232, SEQ ID NO:1233, SEQ ID NO:1234, SEQ ID NO:1235, SEQ IDNO:1236, SEQ ID NO:1237, SEQ ID NO:1238, SEQ ID NO:1239, SEQ ID NO:1240,SEQ ID NO:1241, SEQ ID NO:1242, SEQ ID NO:1243, SEQ ID NO:1244, SEQ IDNO:1245, SEQ ID NO:1246, SEQ ID NO:1247, SEQ ID NO:1248, SEQ ID NO:1249,SEQ ID NO:1251, SEQ ID NO:1253, SEQ ID NO:1255, SEQ ID NO:1257, SEQ IDNO:1259, SEQ ID NO:1261, SEQ ID NO:1263, SEQ ID NO:1264, SEQ ID NO:1265,SEQ ID NO:1266, SEQ ID NO:1267, SEQ ID NO:1268, SEQ ID NO:1269, SEQ IDNO:1270, SEQ ID NO:1271, and SEQ ID NO:1272.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1274, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1274. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1274 areprovided in FIG. 43 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1276, SEQ ID NO:1278, SEQ ID NO:1280, SEQID NO:1281, SEQ ID NO:1282, SEQ ID NO:1284, SEQ ID NO:1285, SEQ IDNO:1287, SEQ ID NO:1289, SEQ ID NO:1291, SEQ ID NO:1293, SEQ ID NO:1294,SEQ ID NO:1295, SEQ ID NO:1296, SEQ ID NO:1297, SEQ ID NO:1298, and SEQID NO:1300.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1302, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1302. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1302 areprovided in FIG. 44 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1303, SEQ ID NO:1305, SEQ ID NO:1307, SEQID NO:1309, SEQ ID NO:1311, SEQ ID NO:1312, SEQ ID NO:1313, SEQ IDNO:1314, SEQ ID NO:1315, SEQ ID NO:1317, SEQ ID NO:1318, SEQ ID NO:1319,SEQ ID NO:1320, SEQ ID NO:1321, SEQ ID NO:1322, SEQ ID NO:1323, SEQ IDNO:1324, SEQ ID NO:1325, SEQ ID NO:1326, SEQ ID NO:1327, SEQ ID NO:1328,SEQ ID NO:1330, SEQ ID NO:1331, SEQ ID NO:1333, SEQ ID NO:1334, SEQ IDNO:1335, SEQ ID NO:1336, SEQ ID NO:1337, SEQ ID NO:1338, SEQ ID NO:1339,and SEQ ID NO:1340.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1342, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1342. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1342 areprovided in FIG. 45 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1344, SEQ ID NO:1346, SEQ ID NO:1348, SEQID NO:1350, SEQ ID NO:1352, SEQ ID NO:1354, SEQ ID NO:1355, SEQ IDNO:1357, SEQ ID NO:1358, SEQ ID NO:1360, SEQ ID NO:1361, SEQ ID NO:1362,SEQ ID NO:1363, SEQ ID NO:1364, SEQ ID NO:1366, SEQ ID NO:1367, SEQ IDNO:1369, SEQ ID NO:1370, SEQ ID NO:1371, SEQ ID NO:1372, SEQ ID NO:1373,SEQ ID NO:1374, SEQ ID NO:1375, SEQ ID NO:1376, SEQ ID NO:1377, SEQ IDNO:1378, SEQ ID NO:1379, SEQ ID NO:1380, SEQ ID NO:1381, SEQ ID NO:1382,and SEQ ID NO:1383.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1385, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1385. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1385 areprovided in FIG. 46 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1387, SEQ ID NO:1389, SEQ ID NO:1390, SEQID NO:1391, SEQ ID NO:1393, SEQ ID NO:1394, SEQ ID NO:1395, SEQ IDNO:1396, SEQ ID NO:1398, SEQ ID NO:1400, SEQ ID NO:1401, SEQ ID NO:1402,SEQ ID NO:1403, SEQ ID NO:1404, SEQ ID NO:1405, and SEQ ID NO:1407.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1409, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1409. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1409 areprovided in FIG. 47 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1411, SEQ ID NO:1413, SEQ ID NO:1415, SEQID NO:1417, SEQ ID NO:1418, SEQ ID NO:1419, SEQ ID NO:1421, SEQ IDNO:1423, SEQ ID NO:1424, SEQ ID NO:1425, and SEQ ID NO:1426.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1428, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1428. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1428 areprovided in FIG. 48 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1430, SEQ ID NO:1432, SEQ ID NO:1434, SEQID NO:1436, SEQ ID NO:1439, SEQ ID NO:1442, SEQ ID NO:1444, SEQ IDNO:1446, SEQ ID NO:1448, SEQ ID NO:1450, SEQ ID NO:1452, SEQ ID NO:1453,SEQ ID NO:1454, SEQ ID NO:1455, SEQ ID NO:1456, SEQ ID NO:1457, SEQ IDNO:1458, and SEQ ID NO:1459.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1463, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1463. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1463 areprovided in FIG. 49 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1465, SEQ ID NO:1467, SEQ ID NO:1469, SEQID NO:1471, SEQ ID NO:1473, SEQ ID NO:1474, SEQ ID NO:1475, SEQ IDNO:1476, and SEQ ID NO:1477.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1491, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1491. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1491 areprovided in FIG. 50 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1493, SEQ ID NO:1495, SEQ ID NO:1497, SEQID NO:1499, SEQ ID NO:1501, SEQ ID NO:1503, SEQ ID NO:1504, SEQ IDNO:1505, SEQ ID NO:1506, and SEQ ID NO:1508.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1510, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1510. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1510 areprovided in FIG. 51 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1512, SEQ ID NO:1514, SEQ ID NO:1516, SEQID NO:1518, SEQ ID NO:1520, SEQ ID NO:1522, and SEQ ID NO:1523.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1525, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1525. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1525 areprovided in FIG. 52 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1527, SEQ ID NO:1529, SEQ ID NO:1530, SEQID NO:1532, SEQ ID NO:1534, and SEQ ID NO:1535.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1537, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1537. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1537 areprovided in FIG. 53 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1539, SEQ ID NO:1540, SEQ ID NO:1541, SEQID NO:1543, SEQ ID NO:1545, SEQ ID NO:1547, SEQ ID NO:1548, SEQ IDNO:1550, SEQ ID NO:1552, SEQ ID NO:2386, SEQ ID NO:2388, SEQ ID NO:2390,SEQ ID NO:2391, and SEQ ID NO:2392.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1554, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1554. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1554 areprovided in FIG. 54 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1555, SEQ ID NO:1557, SEQ ID NO:1559, SEQID NO:1561, SEQ ID NO:1563, SEQ ID NO:1565, SEQ ID NO:1567, SEQ IDNO:1569, SEQ ID NO:1571, SEQ ID NO:1572, SEQ ID NO:1573, SEQ ID NO:1574,and SEQ ID NO:1575.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1577, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1577. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1577 areprovided in FIG. 55 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:1035, SEQ ID NO:1036, SEQ ID NO:1037, SEQID NO:1040, SEQ ID NO:1041, SEQ ID NO:1043, SEQ ID NO:1044, SEQ IDNO:1046, SEQ ID NO:1047, SEQ ID NO:1048, SEQ ID NO:1050, SEQ ID NO:1440,SEQ ID NO:1480, SEQ ID NO:1481, SEQ ID NO:1482, SEQ ID NO:1483, SEQ IDNO:1484, SEQ ID NO:1485, SEQ ID NO:1486, SEQ ID NO:1487, SEQ ID NO:1488,SEQ ID NO:1578, SEQ ID NO:1580, SEQ ID NO:1582, SEQ ID NO:1584, SEQ IDNO:1586, SEQ ID NO:1588, SEQ ID NO:1590, SEQ ID NO:1592, SEQ ID NO:1594,SEQ ID NO:1596, SEQ ID NO:1598, SEQ ID NO:1599, SEQ ID NO:1601, SEQ IDNO:1602, SEQ ID NO:1605, SEQ ID NO:1607, SEQ ID NO:1608, SEQ ID NO:1609,SEQ ID NO:1611, SEQ ID NO:1613, SEQ ID NO:1615, SEQ ID NO:1617, SEQ IDNO:1619, SEQ ID NO:1621, SEQ ID NO:1622, SEQ ID NO:1623, SEQ ID NO:1624,SEQ ID NO:1625, SEQ ID NO:1627, SEQ ID NO:1629, SEQ ID NO:1631, SEQ IDNO:1633, SEQ ID NO:1635, SEQ ID NO:1637, SEQ ID NO:1639, SEQ ID NO:1643,SEQ ID NO:1645, SEQ ID NO:1648, SEQ ID NO:1649, SEQ ID NO:1651, SEQ IDNO:1653.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:1437, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ IDNO:1437. Amino acid sequences of polypeptides having greater than 20%sequence identity to the polypeptide set forth in SEQ ID NO:1437 areprovided in FIG. 56 and in the Sequence Listing. Examples of suchpolypeptides include SEQ ID NO:173, SEQ ID NO:212, SEQ ID NO:361, SEQ IDNO:421, SEQ ID NO:443, SEQ ID NO:740, SEQ ID NO:744, SEQ ID NO:942, SEQID NO:1461.

In some cases, a low nitrogen tolerance-modulating polypeptide has anamino acid sequence with sequence similarity to the amino acid sequenceset forth in SEQ ID NO:97, and preferably has at least 20%, e.g., 50%,52%, 56%, 59%, 61%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99%sequence identity, to the amino acid sequence set forth in SEQ ID NO:97.Amino acid sequences of polypeptides having greater than 20% sequenceidentity to the polypeptide set forth in SEQ ID NO:1437 are provided inFIG. 57 and in the Sequence Listing. Examples of such polypeptidesinclude SEQ ID NO:2010, SEQ ID NO:2011, SEQ ID NO:2013, SEQ ID NO:2015,and SEQ ID NO:2017

E. Other Sequences

It should be appreciated that a low nitrogen tolerance-modulatingpolypeptide can include additional amino acids that are not involved inlow nitrogen tolerance-modulation, and thus such a polypeptide can belonger than would otherwise be the case. For example, a low nitrogentolerance-modulating polypeptide can include a purification tag, achloroplast transit peptide, a mitochondrial transit peptide, anamyloplast peptide, or a leader sequence added to the amino or carboxyterminus. In some embodiments, a low nitrogen tolerance-modulatingpolypeptide includes an amino acid sequence that functions as areporter, e.g., a green fluorescent protein or yellow fluorescentprotein

III. NUCLEIC ACIDS

Nucleic acids described herein include nucleic acids that are effectiveto modulate low-nitrogen tolerance levels when transcribed in a plant orplant cell. Such nucleic acids include, without limitation, those thatencode a low nitrogen tolerance-modulating polypeptide and those thatcan be used to inhibit expression of low nitrogen tolerance-modulatingpolypeptide via a nucleic acid based method.

A. Nucleic Acids Encoding Low Nitrogen Tolerance-Modulating Polypeptides

Nucleic acids encoding low nitrogen tolerance-modulating polypeptidesare described herein. Examples of such nucleic acids include SEQ IDNO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ IDNO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331,SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ IDNO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823,SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ IDNO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ IDNO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209,SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ IDNO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509,SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ ID NO:1576, asdescribed in more detail below. A nucleic acid also can be a fragmentthat is at least 40% (e.g., at least 45, 50, 55, 60, 65, 70, 75, 80, 85,90, 95, or 99%) of the length of the full-length nucleic acid set forthin SEQ ID NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99,SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ IDNO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555,SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ IDNO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890,SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ IDNO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156,SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ IDNO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384,SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ IDNO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ IDNO:1576.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:2.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:2.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO: 48. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO: 48.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO: 48.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:76. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:76.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:76.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:96. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:96.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:96.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:99. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:99.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:99.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:151. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:151.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:151.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:165. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:165.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:165.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:175. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:175.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:175.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:185. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:185.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:185.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:207. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:207.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:207.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:217. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:217.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:217.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:233. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:233.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:233.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:245. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:245.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:245.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:299. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:299.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:299.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:331. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:331.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:331.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:367. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:367.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:367.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:509. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:509.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:509.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:532. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:532.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:532.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:555. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:555.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:555.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:557. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:557.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:557.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:592. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:592.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:592.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:612. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:612.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:612.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:645. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:645.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:645.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:686. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:686.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:686.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:729. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:729.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:729.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:745. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:745.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:745.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:768. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:768.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:768.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:791. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:791.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:791.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:823. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:823.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:823.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:827. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:827.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:827.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:852. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:852.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:852.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:854. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:854.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:854.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:890. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:890.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:890.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:916. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:916.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:916.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:943. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:943.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:943.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:975. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:975.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:975.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:981. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:981.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:981.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO: 1034. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1034. For example, a low nitrogen tolerance-modulating nucleic acid canhave a nucleotide sequence with at least 80% sequence identity, e.g.,81%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to thenucleotide sequence set forth in SEQ ID NO: 1034.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1053. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1053.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1053.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1098. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1098.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1098.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1111. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1111.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1111.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1115. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1115.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1115.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1156. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1156.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1156.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1158. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1158.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1158.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1165. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1165.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1165.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1184. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1184.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1184.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1193. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1193.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1193.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO: 1209. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1209. For example, a low nitrogen tolerance-modulating nucleic acid canhave a nucleotide sequence with at least 80% sequence identity, e.g.,81%, 85%, 90%, 95%, 97%, 98%, or 99% sequence identity, to thenucleotide sequence set forth in SEQ ID NO: 1209.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1273. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1273.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1273.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1301. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1301.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1301.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1341. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1341.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1341.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1384. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1384.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1384.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1408. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1408.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1408.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1427. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1427.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1427.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1462. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1462.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1462.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1490. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1490.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1490.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1509. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1509.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1509.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1524. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1524.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1524.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1536. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1536.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1536.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1553. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1553.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1553.

A low nitrogen tolerance-modulating nucleic acid can comprise thenucleotide sequence set forth in SEQ ID NO:1576. Alternatively, a lownitrogen tolerance-modulating nucleic acid can be a variant of thenucleic acid having the nucleotide sequence set forth in SEQ ID NO:1576.For example, a low nitrogen tolerance-modulating nucleic acid can have anucleotide sequence with at least 80% sequence identity, e.g., 81%, 85%,90%, 95%, 97%, 98%, or 99% sequence identity, to the nucleotide sequenceset forth in SEQ ID NO:1576.

Isolated nucleic acid molecules can be produced by standard techniques.For example, polymerase chain reaction (PCR) techniques can be used toobtain an isolated nucleic acid containing a nucleotide sequencedescribed herein. PCR can be used to amplify specific sequences from DNAas well as RNA, including sequences from total genomic DNA or totalcellular RNA. Various PCR methods are described, for example, in PCRPrimer: A Laboratory Manual, Dieffenbach and Dveksler, eds., Cold SpringHarbor Laboratory Press, 1995. Generally, sequence information from theends of the region of interest or beyond is employed to designoligonucleotide primers that are identical or similar in sequence toopposite strands of the template to be amplified. Various PCR strategiesalso are available by which site-specific nucleotide sequencemodifications can be introduced into a template nucleic acid. Isolatednucleic acids also can be chemically synthesized, either as a singlenucleic acid molecule (e.g., using automated DNA synthesis in the 3′ to5′ direction using phosphoramidite technology) or as a series ofoligonucleotides. For example, one or more pairs of longoligonucleotides (e.g., >100 nucleotides) can be synthesized thatcontain the desired sequence, with each pair containing a short segmentof complementarity (e.g., about 15 nucleotides) such that a duplex isformed when the oligonucleotide pair is annealed. DNA polymerase is usedto extend the oligonucleotides, resulting in a single, double-strandednucleic acid molecule per oligonucleotide pair, which then can beligated into a vector. Isolated nucleic acids of the invention also canbe obtained by mutagenesis of, e.g., a naturally occurring DNA.

B. Use of Nucleic Acids to Modulate Expression of Polypeptides

i. Expression of a Low Nitrogen Tolerance-Modulating Polypeptide

A nucleic acid encoding one of the low nitrogen tolerance-modulatingpolypeptides described herein can be used to express the polypeptide ina plant species of interest, typically by transforming a plant cell witha nucleic acid having the coding sequence for the polypeptide operablylinked in sense orientation to one or more regulatory regions. It willbe appreciated that because of the degeneracy of the genetic code, anumber of nucleic acids can encode a particular low nitrogentolerance-modulating polypeptide; i.e., for many amino acids, there ismore than one nucleotide triplet that serves as the codon for the aminoacid. Thus, codons in the coding sequence for a given low nitrogentolerance-modulating polypeptide can be modified such that optimalexpression in a particular plant species is obtained, using appropriatecodon bias tables for that species.

In some cases, expression of a low nitrogen tolerance-modulatingpolypeptide inhibits one or more functions of an endogenous polypeptide.For example, a nucleic acid that encodes a dominant negative polypeptidecan be used to inhibit protein function. A dominant negative polypeptidetypically is mutated or truncated relative to an endogenous wild typepolypeptide, and its presence in a cell inhibits one or more functionsof the wild type polypeptide in that cell, i.e., the dominant negativepolypeptide is genetically dominant and confers a loss of function. Themechanism by which a dominant negative polypeptide confers such aphenotype can vary but often involves a protein-protein interaction or aprotein-DNA interaction. For example, a dominant negative polypeptidecan be an enzyme that is truncated relative to a native wild typeenzyme, such that the truncated polypeptide retains domains involved inbinding a first protein but lacks domains involved in binding a secondprotein. The truncated polypeptide is thus unable to properly modulatethe activity of the second protein. See, e.g., US 2007/0056058. Asanother example, a point mutation that results in a non-conservativeamino acid substitution in a catalytic domain can result in a dominantnegative polypeptide. See, e.g., US 2005/032221. As another example, adominant negative polypeptide can be a transcription factor that istruncated relative to a native wild type transcription factor, such thatthe truncated polypeptide retains the DNA binding domain(s) but lacksthe activation domain(s). Such a truncated polypeptide can inhibit thewild type transcription factor from binding DNA, thereby inhibitingtranscription activation.

ii. Inhibition of Expression of a Low Nitrogen Tolerance-ModulatingPolypeptide

Polynucleotides and recombinant constructs described herein can be usedto inhibit expression of a low nitrogen tolerance-modulating polypeptidein a plant species of interest. See, e.g., Matzke and Birchler, NatureReviews Genetics 6:24-35 (2005); Akashi et al., Nature Reviews Mol. CellBiology 6:413-422 (2005); Mittal, Nature Reviews Genetics 5:355-365(2004); Dorsett and Tuschl, Nature Reviews Drug Discovery 3: 318-329(2004); and Nature Reviews RNA interference collection, October 2005 atnature.com/reviews/focus/mai. A number of nucleic acid based methods,including antisense RNA, ribozyme directed RNA cleavage,post-transcriptional gene silencing (PTGS), e.g., RNA interference(RNAi), and transcriptional gene silencing (TGS) are known to inhibitgene expression in plants. Suitable polynucleotides include full-lengthnucleic acids encoding low nitrogen tolerance-modulating polypeptides orfragments of such full-length nucleic acids. In some embodiments, acomplement of the full-length nucleic acid or a fragment thereof can beused. Typically, a fragment is at least 10 nucleotides, e.g., at least12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 35,40, 50, 80, 100, 200, 500 nucleotides or more. Generally, higherhomology can be used to compensate for the use of a shorter sequence.

Antisense technology is one well-known method. In this method, a nucleicacid of a gene to be repressed is cloned and operably linked to aregulatory region and a transcription termination sequence so that theantisense strand of RNA is transcribed. The recombinant construct isthen transformed into plants, as described herein, and the antisensestrand of RNA is produced. The nucleic acid need not be the entiresequence of the gene to be repressed, but typically will besubstantially complementary to at least a portion of the sense strand ofthe gene to be repressed.

In another method, a nucleic acid can be transcribed into a ribozyme, orcatalytic RNA, that affects expression of an mRNA. See, U.S. Pat. No.6,423,885. Ribozymes can be designed to specifically pair with virtuallyany target RNA and cleave the phosphodiester backbone at a specificlocation, thereby functionally inactivating the target RNA. Heterologousnucleic acids can encode ribozymes designed to cleave particular mRNAtranscripts, thus preventing expression of a polypeptide. Hammerheadribozymes are useful for destroying particular mRNAs, although variousribozymes that cleave mRNA at site-specific recognition sequences can beused. Hammerhead ribozymes cleave mRNAs at locations dictated byflanking regions that form complementary base pairs with the targetmRNA. The sole requirement is that the target RNA contains a 5′-UG-3′nucleotide sequence. The construction and production of hammerheadribozymes is known in the art. See, for example, U.S. Pat. No. 5,254,678and WO 02/46449 and references cited therein. Hammerhead ribozymesequences can be embedded in a stable RNA such as a transfer RNA (tRNA)to increase cleavage efficiency in vivo. Perriman et al. (1995) Proc.Natl. Acad. Sci. USA, 92(13):6175-6179; de Feyter and Gaudron, Methodsin Molecular Biology, Vol. 74, Chapter 43, “Expressing Ribozymes inPlants”, Edited by Turner, P. C., Humana Press Inc., Totowa, N.J. RNAendoribonucleases which have been described, such as the one that occursnaturally in Tetrahymena thermophila, can be useful. See, for example,U.S. Pat. Nos. 4,987,071 and 6,423,885.

PTGS, e.g., RNAi, can also be used to inhibit the expression of a gene.For example, a construct can be prepared that includes a sequence thatis transcribed into an RNA that can anneal to itself, e.g., a doublestranded RNA having a stem-loop structure. In some embodiments, onestrand of the stem portion of a double stranded RNA comprises a sequencethat is similar or identical to the sense coding sequence or a fragmentthereof of a low nitrogen tolerance-modulating polypeptide, and that isfrom about 10 nucleotides to about 2,500 nucleotides in length. Thelength of the sequence that is similar or identical to the sense codingsequence can be from 10 nucleotides to 500 nucleotides, from 15nucleotides to 300 nucleotides, from 20 nucleotides to 100 nucleotides,or from 25 nucleotides to 100 nucleotides. The other strand of the stemportion of a double stranded RNA comprises a sequence that is similar oridentical to the antisense strand or a fragment thereof of the codingsequence of the low nitrogen tolerance-modulating polypeptide, and canhave a length that is shorter, the same as, or longer than thecorresponding length of the sense sequence. In some cases, one strand ofthe stem portion of a double stranded RNA comprises a sequence that issimilar or identical to the 3′ or 5′ untranslated region, or a fragmentthereof, of an mRNA encoding a low nitrogen tolerance-modulatingpolypeptide, and the other strand of the stem portion of the doublestranded RNA comprises a sequence that is similar or identical to thesequence that is complementary to the 3′ or 5′ untranslated region,respectively, or a fragment thereof, of the mRNA encoding the lownitrogen tolerance-modulating polypeptide. In other embodiments, onestrand of the stem portion of a double stranded RNA comprises a sequencethat is similar or identical to the sequence of an intron, or a fragmentthereof, in the pre-mRNA encoding a low nitrogen tolerance-modulatingpolypeptide, and the other strand of the stem portion comprises asequence that is similar or identical to the sequence that iscomplementary to the sequence of the intron, or a fragment thereof, inthe pre-mRNA.

The loop portion of a double stranded RNA can be from 3 nucleotides to5,000 nucleotides, e.g., from 3 nucleotides to 25 nucleotides, from 15nucleotides to 1,000 nucleotides, from 20 nucleotides to 500nucleotides, or from 25 nucleotides to 200 nucleotides. The loop portionof the RNA can include an intron or a fragment thereof. A doublestranded RNA can have zero, one, two, three, four, five, six, seven,eight, nine, ten, or more stem-loop structures.

A construct including a sequence that is operably linked to a regulatoryregion and a transcription termination sequence, and that is transcribedinto an RNA that can form a double stranded RNA, is transformed intoplants as described herein. Methods for using RNAi to inhibit theexpression of a gene are known to those of skill in the art. See, e.g.,U.S. Pat. Nos. 5,034,323; 6,326,527; 6,452,067; 6,573,099; 6,753,139;and 6,777,588. See also WO 97/01952; WO 98/53083; WO 99/32619; WO98/36083; and U.S. Patent Publications 20030175965, 20030175783,20040214330, and 20030180945.

Constructs containing regulatory regions operably linked to nucleic acidmolecules in sense orientation can also be used to inhibit theexpression of a gene. The transcription product can be similar oridentical to the sense coding sequence, or a fragment thereof, of a lownitrogen tolerance-modulating polypeptide. The transcription productalso can be unpolyadenylated, lack a 5′ cap structure, or contain anunspliceable intron. Methods of inhibiting gene expression using afull-length cDNA as well as a partial cDNA sequence are known in theart. See, e.g., U.S. Pat. No. 5,231,020.

In some embodiments, a construct containing a nucleic acid having atleast one strand that is a template for both sense and antisensesequences that are complementary to each other is used to inhibit theexpression of a gene. The sense and antisense sequences can be part of alarger nucleic acid molecule or can be part of separate nucleic acidmolecules having sequences that are not complementary. The sense orantisense sequence can be a sequence that is identical or complementaryto the sequence of an mRNA, the 3′ or 5′ untranslated region of an mRNA,or an intron in a pre-mRNA encoding a low nitrogen tolerance-modulatingpolypeptide, or a fragment of such sequences. In some embodiments, thesense or antisense sequence is identical or complementary to a sequenceof the regulatory region that drives transcription of the gene encodinga low nitrogen tolerance-modulating polypeptide. In each case, the sensesequence is the sequence that is complementary to the antisensesequence.

The sense and antisense sequences can be any length greater than about10 nucleotides (e.g., 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, or more nucleotides). For example, anantisense sequence can be 21 or 22 nucleotides in length. Typically, thesense and antisense sequences range in length from about 15 nucleotidesto about 30 nucleotides, e.g., from about 18 nucleotides to about 28nucleotides, or from about 21 nucleotides to about 25 nucleotides.

In some embodiments, an antisense sequence is a sequence complementaryto an mRNA sequence, or a fragment thereof, encoding a low nitrogentolerance-modulating polypeptide described herein. The sense sequencecomplementary to the antisense sequence can be a sequence present withinthe mRNA of the low nitrogen tolerance-modulating polypeptide.Typically, sense and antisense sequences are designed to correspond to a15-30 nucleotide sequence of a target mRNA such that the level of thattarget mRNA is reduced.

In some embodiments, a construct containing a nucleic acid having atleast one strand that is a template for more than one sense sequence(e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more sense sequences) can be usedto inhibit the expression of a gene. Likewise, a construct containing anucleic acid having at least one strand that is a template for more thanone antisense sequence (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or moreantisense sequences) can be used to inhibit the expression of a gene.For example, a construct can contain a nucleic acid having at least onestrand that is a template for two sense sequences and two antisensesequences. The multiple sense sequences can be identical or different,and the multiple antisense sequences can be identical or different. Forexample, a construct can have a nucleic acid having one strand that is atemplate for two identical sense sequences and two identical antisensesequences that are complementary to the two identical sense sequences.Alternatively, an isolated nucleic acid can have one strand that is atemplate for (1) two identical sense sequences 20 nucleotides in length,(2) one antisense sequence that is complementary to the two identicalsense sequences 20 nucleotides in length, (3) a sense sequence 30nucleotides in length, and (4) three identical antisense sequences thatare complementary to the sense sequence 30 nucleotides in length. Theconstructs provided herein can be designed to have any arrangement ofsense and antisense sequences. For example, two identical sensesequences can be followed by two identical antisense sequences or can bepositioned between two identical antisense sequences.

A nucleic acid having at least one strand that is a template for one ormore sense and/or antisense sequences can be operably linked to aregulatory region to drive transcription of an RNA molecule containingthe sense and/or antisense sequence(s). In addition, such a nucleic acidcan be operably linked to a transcription terminator sequence, such asthe terminator of the nopaline synthase (nos) gene. In some cases, tworegulatory regions can direct transcription of two transcripts: one fromthe top strand, and one from the bottom strand. See, for example, Yan etal., Plant Physiol., 141:1508-1518 (2006). The two regulatory regionscan be the same or different. The two transcripts can formdouble-stranded RNA molecules that induce degradation of the target RNA.In some cases, a nucleic acid can be positioned within a T-DNA orplant-derived transfer DNA (P-DNA) such that the left and right T-DNAborder sequences, or the left and right border-like sequences of theP-DNA, flank or are on either side of the nucleic acid. See, US2006/0265788. The nucleic acid sequence between the two regulatoryregions can be from about 15 to about 300 nucleotides in length. In someembodiments, the nucleic acid sequence between the two regulatoryregions is from about 15 to about 200 nucleotides in length, from about15 to about 100 nucleotides in length, from about 15 to about 50nucleotides in length, from about 18 to about 50 nucleotides in length,from about 18 to about 40 nucleotides in length, from about 18 to about30 nucleotides in length, or from about 18 to about 25 nucleotides inlength.

In some nucleic-acid based methods for inhibition of gene expression inplants, a suitable nucleic acid can be a nucleic acid analog. Nucleicacid analogs can be modified at the base moiety, sugar moiety, orphosphate backbone to improve, for example, stability, hybridization, orsolubility of the nucleic acid. Modifications at the base moiety includedeoxyuridine for deoxythymidine, and 5-methyl-2′-deoxycytidine and5-bromo-2′-deoxycytidine for deoxycytidine. Modifications of the sugarmoiety include modification of the 2′ hydroxyl of the ribose sugar toform 2′-O-methyl or 2′-O-allyl sugars. The deoxyribose phosphatebackbone can be modified to produce morpholino nucleic acids, in whicheach base moiety is linked to a six-membered morpholino ring, or peptidenucleic acids, in which the deoxyphosphate backbone is replaced by apseudopeptide backbone and the four bases are retained. See, forexample, Summerton and Weller (1997) Antisense Nucleic Acid Drug Dev.,7:187-195; Hyrup et al. (1996) Bioorgan. Med. Chem., 4:5-23. Inaddition, the deoxyphosphate backbone can be replaced with, for example,a phosphorothioate or phosphorodithioate backbone, a phosphoroamidite,or an alkyl phosphotriester backbone.

C. Constructs/Vectors

Recombinant constructs provided herein can be used to transform plantsor plant cells in order to modulate low-nitrogen tolerance levels. Arecombinant nucleic acid construct can comprise a nucleic acid encodinga low nitrogen tolerance-modulating polypeptide as described herein,operably linked to a regulatory region suitable for expressing the lownitrogen tolerance-modulating polypeptide in the plant or cell. Thus, anucleic acid can comprise a coding sequence that encodes any of the lownitrogen tolerance-modulating polypeptides as set forth in SEQ ID NO:3,SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152,SEQ ID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ IDNO:234, SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQID NO:510, SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593,SEQ ID NO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ IDNO:746, SEQ ID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQID NO:853, SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944,SEQ ID NO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ IDNO:1112, SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166,SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ IDNO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428,SEQ ID NO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ IDNO:1525, SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577. Examples ofnucleic acids encoding low nitrogen tolerance-modulating polypeptidesare set forth in SEQ ID NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96,SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ IDNO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532,SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ IDNO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854,SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ IDNO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115,SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ IDNO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341,SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ IDNO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553,and SEQ ID NO:1576. The low nitrogen tolerance-modulating polypeptideencoded by a recombinant nucleic acid can be a native low nitrogentolerance-modulating polypeptide, or can be heterologous to the cell. Insome cases, the recombinant construct contains a nucleic acid thatinhibits expression of a low nitrogen tolerance-modulating polypeptide,operably linked to a regulatory region. Examples of suitable regulatoryregions are described in the section entitled “Regulatory Regions.”

Vectors containing recombinant nucleic acid constructs such as thosedescribed herein also are provided. Suitable vector backbones include,for example, those routinely used in the art such as plasmids, viruses,artificial chromosomes, BACs, YACs, or PACs. Suitable expression vectorsinclude, without limitation, plasmids and viral vectors derived from,for example, bacteriophage, baculoviruses, and retroviruses. Numerousvectors and expression systems are commercially available from suchcorporations as Novagen (Madison, Wis.), Clontech (Palo Alto, Calif.),Stratagene (La Jolla, Calif.), and Invitrogen/Life Technologies(Carlsbad, Calif.).

The vectors provided herein also can include, for example, origins ofreplication, scaffold attachment regions (SARs), and/or markers. Amarker gene can confer a selectable phenotype on a plant cell. Forexample, a marker can confer biocide resistance, such as resistance toan antibiotic (e.g., kanamycin, G418, bleomycin, or hygromycin), or anherbicide (e.g., glyphosate, chlorsulfuron or phosphinothricin). Inaddition, an expression vector can include a tag sequence designed tofacilitate manipulation or detection (e.g., purification orlocalization) of the expressed polypeptide. Tag sequences, such asluciferase, β-glucuronidase (GUS), green fluorescent protein (GFP),glutathione S-transferase (GST), polyhistidine, c-myc, hemagglutinin, orFlag™ tag (Kodak, New Haven, Conn.) sequences typically are expressed asa fusion with the encoded polypeptide. Such tags can be insertedanywhere within the polypeptide, including at either the carboxyl oramino terminus.

D. Regulatory Regions

The choice of regulatory regions to be included in a recombinantconstruct depends upon several factors, including, but not limited to,efficiency, selectability, inducibility, desired expression level, andcell- or tissue-preferential expression. It is a routine matter for oneof skill in the art to modulate the expression of a coding sequence byappropriately selecting and positioning regulatory regions relative tothe coding sequence. Transcription of a nucleic acid can be modulated ina similar manner.

Some suitable regulatory regions initiate transcription only, orpredominantly, in certain cell types. Methods for identifying andcharacterizing regulatory regions in plant genomic DNA are known,including, for example, those described in the following references:Jordano et al. (1989) Plant Cell, 1:855-866; Bustos et al. (1989) PlantCell, 1:839-854; Green et al. (1988) EMBO J., 7:4035-4044; Meier et al.(1991) Plant Cell, 3:309-316; and Zhang et al. (1996) Plant Physiology,110:1069-1079.

Examples of various classes of regulatory regions are described below.Some of the regulatory regions indicated below as well as additionalregulatory regions are described in more detail in U.S. PatentApplication Ser. Nos. 60/505,689; 60/518,075; 60/544,771; 60/558,869;60/583,691; 60/619,181; 60/637,140; 60/757,544; 60/776,307; 10/957,569;11/058,689; 11/172,703; 11/208,308; 11/274,890; 60/583,609; 60/612,891;11/097,589; 11/233,726; 11/408,791; 11/414,142; 10/950,321; 11/360,017;PCT/US05/011105; PCT/US05/23639; PCT/US05/034308; PCT/US05/034343; andPCT/US06/038236; PCT/US06/040572; and PCT/US07/62762.

For example, the sequences of regulatory regions p326, YP0144, YP0190,p13879, YP0050, p32449, 21876, YP0158, YP0214, YP0380, PT0848, PT0633,YP0128, YP0275, PT0660, PT0683, PT0758, PT0613, PT0672, PT0688, PT0837,YP0092, PT0676, PT0708, YP0396, YP0007, YP0111, YP0103, YP0028, YP0121,YP0008, YP0039, YP0115, YP0119, YP0120, YP0374, YP0101, YP0102, YP0110,YP0117, YP0137, YP0285, YP0212, YP0097, YP0107, YP0088, YP0143, YP0156,PT0650, PT0695, PT0723, PT0838, PT0879, PT0740, PT0535, PT0668, PT0886,PT0585, YP0381, YP0337, PT0710, YP0356, YP0385, YP0384, YP0286, YP0377,PD1367, PT0863, PT0829, PT0665, PT0678, YP0086, YP0188, YP0263, PT0743and YP0096 are set forth in the sequence listing of PCT/US06/040572; thesequence of regulatory region PT0625 is set forth in the sequencelisting of PCT/US05/034343; the sequences of regulatory regions PT0623,YP0388, YP0087, YP0093, YP0108, YP0022 and YP0080 are set forth in thesequence listing of U.S. patent application Ser. No. 11/172,703; thesequence of regulatory region PR0924 is set forth in the sequencelisting of PCT/US07/62762; and the sequences of regulatory regionsp530c10, pOsFIE2-2, pOsMEA, pOsYp102, and pOsYp285 are set forth in thesequence listing of PCT/US06/038236.

It will be appreciated that a regulatory region may meet criteria forone classification based on its activity in one plant species, and yetmeet criteria for a different classification based on its activity inanother plant species.

i. Broadly Expressing Promoters

A promoter can be said to be “broadly expressing” when it promotestranscription in many, but not necessarily all, plant tissues. Forexample, a broadly expressing promoter can promote transcription of anoperably linked sequence in one or more of the shoot, shoot tip (apex),and leaves, but weakly or not at all in tissues such as roots or stems.As another example, a broadly expressing promoter can promotetranscription of an operably linked sequence in one or more of the stem,shoot, shoot tip (apex), and leaves, but can promote transcriptionweakly or not at all in tissues such as reproductive tissues of flowersand developing seeds. Non-limiting examples of broadly expressingpromoters that can be included in the nucleic acid constructs providedherein include the p326, YP0144, YP0190, p13879, YP0050, p32449, 21876,YP0158, YP0214, YP0380, PT0848, and PT0633 promoters. Additionalexamples include the cauliflower mosaic virus (CaMV) 35S promoter, themannopine synthase (MAS) promoter, the 1′ or 2′ promoters derived fromT-DNA of Agrobacterium tumefaciens, the figwort mosaic virus 34Spromoter, actin promoters such as the rice actin promoter, and ubiquitinpromoters such as the maize ubiquitin-1 promoter. In some cases, theCaMV 35S promoter is excluded from the category of broadly expressingpromoters.

ii. Root Promoters

Root-active promoters confer transcription in root tissue, e.g., rootendodermis, root epidermis, or root vascular tissues. In someembodiments, root-active promoters are root-preferential promoters,i.e., confer transcription only or predominantly in root tissue.Root-preferential promoters include the YP0128, YP0275, PT0625, PT0660,PT0683, and PT0758 promoters. Other root-preferential promoters includethe PT0613, PT0672, PT0688, and PT0837 promoters, which drivetranscription primarily in root tissue and to a lesser extent in ovulesand/or seeds. Other examples of root-preferential promoters include theroot-specific subdomains of the CaMV 35S promoter (Lam et al. (1989)Proc. Natl. Acad. Sci. USA, 86:7890-7894), root cell specific promotersreported by Conkling et al. (1990) Plant Physiol., 93:1203-1211, and thetobacco RD2 promoter.

iii. Maturing Endosperm Promoters

In some embodiments, promoters that drive transcription in maturingendosperm can be useful. Transcription from a maturing endospermpromoter typically begins after fertilization and occurs primarily inendosperm tissue during seed development and is typically highest duringthe cellularization phase. Most suitable are promoters that are activepredominantly in maturing endosperm, although promoters that are alsoactive in other tissues can sometimes be used. Non-limiting examples ofmaturing endosperm promoters that can be included in the nucleic acidconstructs provided herein include the napin promoter, the Arcelin-5promoter, the phaseolin promoter (Bustos et al. (1989) Plant Cell,1(9):839-853), the soybean trypsin inhibitor promoter (Riggs et al.(1989) Plant Cell, 1(6):609-621), the ACP promoter (Baerson et al.(1993) Plant Mol. Biol., 22(2):255-267), the stearoyl-ACP desaturasepromoter (Slocombe et al. (1994) Plant Physiol., 104(4):167-176), thesoybean α′ subunit of β-conglycinin promoter (Chen et al. (1986) Proc.Natl. Acad. Sci. USA, 83:8560-8564), the oleosin promoter (Hong et al.(1997) Plant Mol. Biol., 34(3):549-555), and zein promoters, such as the15 kD zein promoter, the 16 kD zein promoter, 19 kD zein promoter, 22 kDzein promoter and 27 kD zein promoter. Also suitable are the Osgt-1promoter from the rice glutelin-1 gene (Zheng et al. (1993) Mol. CellBiol., 13:5829-5842), the beta-amylase promoter, and the barley hordeinpromoter. Other maturing endosperm promoters include the YP0092, PT0676,and PT0708 promoters iv. Ovary Tissue Promoters

Promoters that are active in ovary tissues such as the ovule wall andmesocarp can also be useful, e.g., a polygalacturonidase promoter, thebanana TRX promoter, the melon actin promoter, YP0396, and PT0623.Examples of promoters that are active primarily in ovules includeYP0007, YP0111, YP0092, YP0103, YP0028, YP0121, YP0008, YP0039, YP0115,YP0119, YP0120, and YP0374.

v. Embryo Sac/Early Endosperm Promoters

To achieve expression in embryo sac/early endosperm, regulatory regionscan be used that are active in polar nuclei and/or the central cell, orin precursors to polar nuclei, but not in egg cells or precursors to eggcells. Most suitable are promoters that drive expression only orpredominantly in polar nuclei or precursors thereto and/or the centralcell. A pattern of transcription that extends from polar nuclei intoearly endosperm development can also be found with embryo sac/earlyendosperm-preferential promoters, although transcription typicallydecreases significantly in later endosperm development during and afterthe cellularization phase. Expression in the zygote or developing embryotypically is not present with embryo sac/early endosperm promoters.

Promoters that may be suitable include those derived from the followinggenes: Arabidopsis viviparous-1 (see, GenBank No. U93215); Arabidopsisatmycl (see, Urao (1996) Plant Mol. Biol., 32:571-57; Conceicao (1994)Plant, 5:493-505); Arabidopsis FIE (GenBank No. AF129516); ArabidopsisMEA; Arabidopsis FIS2 (GenBank No. AF096096); and FIE 1.1 (U.S. Pat. No.6,906,244). Other promoters that may be suitable include those derivedfrom the following genes: maize MAC1 (see, Sheridan (1996) Genetics,142:1009-1020); maize Cat3 (see, GenBank No. L05934; Abler (1993) PlantMol. Biol., 22:10131-1038). Other promoters include the followingArabidopsis promoters: YP0039, YP0101, YP0102, YP0110, YP0117, YP0119,YP0137, DME, YP0285, and YP0212. Other promoters that may be usefulinclude the following rice promoters: p530c10, pOsFIE2-2, pOsMEA,pOsYp102, and pOsYp285.

vi. Embryo Promoters

Regulatory regions that preferentially drive transcription in zygoticcells following fertilization can provide embryo-preferentialexpression. Most suitable are promoters that preferentially drivetranscription in early stage embryos prior to the heart stage, butexpression in late stage and maturing embryos is also suitable.Embryo-preferential promoters include the barley lipid transfer protein(Ltp1) promoter (Plant Cell Rep (2001) 20:647-654), YP0097, YP0107,YP0088, YP0143, YP0156, PT0650, PT0695, PT0723, PT0838, PT0879, andPT0740.

vii. Photosynthetic Tissue Promoters

Promoters active in photosynthetic tissue confer transcription in greentissues such as leaves and stems. Most suitable are promoters that driveexpression only or predominantly in such tissues. Examples of suchpromoters include the ribulose-1,5-bisphosphate carboxylase (RbcS)promoters such as the RbcS promoter from eastern larch (Larix laricina),the pine cab6 promoter (Yamamoto et al. (1994) Plant Cell Physiol.,35:773-778), the Cab-1 promoter from wheat (Fejes et al. (1990) PlantMol. Biol., 15:921-932), the CAB-1 promoter from spinach (Lubberstedt etal. (1994) Plant Physiol., 104:997-1006), the cab1R promoter from rice(Luan et al. (1992) Plant Cell, 4:971-981), the pyruvate orthophosphatedikinase (PPDK) promoter from corn (Matsuoka et al. (1993) Proc. Natl.Acad. Sci. USA, 90:9586-9590), the tobacco Lhcb1*2 promoter (Cerdan etal. (1997) Plant Mol. Biol., 33:245-255), the Arabidopsis thaliana SUC2sucrose-H+ symporter promoter (Truernit et al. (1995) Planta,196:564-570), and thylakoid membrane protein promoters from spinach(psaD, psaF, psaE, PC, FNR, atpC, atpD, cab, rbcS). Other photosynthetictissue promoters include PT0535, PT0668, PT0886, YP0144, YP0380 andPT0585.

viii. Vascular Tissue Promoters

Examples of promoters that have high or preferential activity invascular bundles include YP0087, YP0093, YP0108, YP0022, and YP0080.Other vascular tissue-preferential promoters include the glycine-richcell wall protein GRP 1.8 promoter (Keller and Baumgartner (1991) PlantCell, 3(10): 1051-1061), the Commelina yellow mottle virus (CoYMV)promoter (Medberry et al. (1992) Plant Cell, 4(2):185-192), and the ricetungro bacilliform virus (RTBV) promoter (Dai et al. (2004) Proc. Natl.Acad. Sci. USA, 101(2):687-692).

ix. Inducible Promoters

Inducible promoters confer transcription in response to external stimulisuch as chemical agents or environmental stimuli. For example, induciblepromoters can confer transcription in response to hormones such asgiberellic acid or ethylene, or in response to light or drought.Examples of drought-inducible promoters include YP0380, PT0848, YP0381,YP0337, PT0633, YP0374, PT0710, YP0356, YP0385, YP0396, YP0388, YP0384,PT0688, YP0286, YP0377, PD1367, and PD0901. Examples ofnitrogen-inducible promoters include PT0863, PT0829, PT0665, and PT0886.Examples of shade-inducible promoters include PR0924 and PT0678. Anexample of a promoter induced by salt is rd29A (Kasuga et al. (1999)Nature Biotech 17: 287-291).

x. Basal Promoters

A basal promoter is the minimal sequence necessary for assembly of atranscription complex required for transcription initiation. Basalpromoters frequently include a “TATA box” element that may be locatedbetween about 15 and about 35 nucleotides upstream from the site oftranscription initiation. Basal promoters also may include a “CCAAT box”element (typically the sequence CCAAT) and/or a GGGCG sequence, whichcan be located between about 40 and about 200 nucleotides, typicallyabout 60 to about 120 nucleotides, upstream from the transcription startsite.

xi. Stem Promoters

A stem promoter may be specific to one or more stem tissues or specificto stem and other plant parts. Stem promoters may have high orpreferential activity in, for example, epidermis and cortex, vascularcambium, procambium, or xylem. Examples of stem promoters include YP0018which is disclosed in US20060015970 and CryIA(b) and CryIA(c) (Braga etal. 2003, Journal of New Seeds 5:209-221).

xii. Other Promoters

Other classes of promoters include, but are not limited to,shoot-preferential, callus-preferential, trichome cell-preferential,guard cell-preferential such as PT0678, tuber-preferential, parenchymacell-preferential, and senescence-preferential promoters. Promotersdesignated YP0086, YP0188, YP0263, PT0758, PT0743, PT0829, YP0119, andYP0096, as described in the above-referenced patent applications, mayalso be useful.

xiii. Other Regulatory Regions

A 5′ untranslated region (UTR) can be included in nucleic acidconstructs described herein. A 5′ UTR is transcribed, but is nottranslated, and lies between the start site of the transcript and thetranslation initiation codon and may include the +1 nucleotide. A 3′ UTRcan be positioned between the translation termination codon and the endof the transcript. UTRs can have particular functions such as increasingmRNA stability or attenuating translation. Examples of 3′ UTRs include,but are not limited to, polyadenylation signals and transcriptiontermination sequences, e.g., a nopaline synthase termination sequence.

It will be understood that more than one regulatory region may bepresent in a recombinant polynucleotide, e.g., introns, enhancers,upstream activation regions, transcription terminators, and inducibleelements. Thus, for example, more than one regulatory region can beoperably linked to the sequence of a polynucleotide encoding a lownitrogen tolerance-modulating polypeptide.

Regulatory regions, such as promoters for endogenous genes, can beobtained by chemical synthesis or by subcloning from a genomic DNA thatincludes such a regulatory region. A nucleic acid comprising such aregulatory region can also include flanking sequences that containrestriction enzyme sites that facilitate subsequent manipulation.

IV. TRANSGENIC PLANTS AND PLANT CELLS

A. Transformation

The invention also features transgenic plant cells and plants comprisingat least one recombinant nucleic acid construct described herein. Aplant or plant cell can be transformed by having a construct integratedinto its genome, i.e., can be stably transformed. Stably transformedcells typically retain the introduced nucleic acid with each celldivision. A plant or plant cell can also be transiently transformed suchthat the construct is not integrated into its genome. Transientlytransformed cells typically lose all or some portion of the introducednucleic acid construct with each cell division such that the introducednucleic acid cannot be detected in daughter cells after a sufficientnumber of cell divisions. Both transiently transformed and stablytransformed transgenic plants and plant cells can be useful in themethods described herein.

Transgenic plant cells used in methods described herein can constitutepart or all of a whole plant. Such plants can be grown in a mannersuitable for the species under consideration, either in a growthchamber, a greenhouse, or in a field. Transgenic plants can be bred asdesired for a particular purpose, e.g., to introduce a recombinantnucleic acid into other lines, to transfer a recombinant nucleic acid toother species, or for further selection of other desirable traits.Alternatively, transgenic plants can be propagated vegetatively forthose species amenable to such techniques. As used herein, a transgenicplant also refers to progeny of an initial transgenic plant provided theprogeny inherits the transgene. Seeds produced by a transgenic plant canbe grown and then selfed (or outcrossed and selfed) to obtain seedshomozygous for the nucleic acid construct.

Transgenic plants can be grown in suspension culture, or tissue or organculture. For the purposes of this invention, solid and/or liquid tissueculture techniques can be used. When using solid medium, transgenicplant cells can be placed directly onto the medium or can be placed ontoa filter that is then placed in contact with the medium. When usingliquid medium, transgenic plant cells can be placed onto a flotationdevice, e.g., a porous membrane that contacts the liquid medium. A solidmedium can be, for example, Murashige and Skoog (MS) medium containingagar and a suitable concentration of an auxin, e.g.,2,4-dichlorophenoxyacetic acid (2,4-D), and a suitable concentration ofa cytokinin, e.g., kinetin.

When transiently transformed plant cells are used, a reporter sequenceencoding a reporter polypeptide having a reporter activity can beincluded in the transformation procedure and an assay for reporteractivity or expression can be performed at a suitable time aftertransformation. A suitable time for conducting the assay typically isabout 1-21 days after transformation, e.g., about 1-14 days, about 1-7days, or about 1-3 days. The use of transient assays is particularlyconvenient for rapid analysis in different species, or to confirmexpression of a heterologous low nitrogen tolerance-modulatingpolypeptide whose expression has not previously been confirmed inparticular recipient cells.

Techniques for introducing nucleic acids into monocotyledonous anddicotyledonous plants are known in the art, and include, withoutlimitation, Agrobacterium-mediated transformation, viral vector-mediatedtransformation, electroporation and particle gun transformation, e.g.,U.S. Pat. Nos. 5,538,880; 5,204,253; 6,329,571 and 6,013,863. If a cellor cultured tissue is used as the recipient tissue for transformation,plants can be regenerated from transformed cultures if desired, bytechniques known to those skilled in the art.

B. Screening/Selection

A population of transgenic plants can be screened and/or selected forthose members of the population that have a trait or phenotype conferredby expression of the transgene. For example, a population of progeny ofa single transformation event can be screened for those plants having adesired level of expression of a low nitrogen tolerance-modulatingpolypeptide or nucleic acid. Physical and biochemical methods can beused to identify expression levels. These include Southern analysis orPCR amplification for detection of a polynucleotide; Northern blots, S1RNase protection, primer-extension, or RT-PCR amplification fordetecting RNA transcripts; enzymatic assays for detecting enzyme orribozyme activity of polypeptides and polynucleotides; and protein gelelectrophoresis, Western blots, immunoprecipitation, and enzyme-linkedimmunoassays to detect polypeptides. Other techniques such as in situhybridization, enzyme staining, and immunostaining also can be used todetect the presence or expression of polypeptides and/orpolynucleotides. Methods for performing all of the referenced techniquesare known. As an alternative, a population of plants comprisingindependent transformation events can be screened for those plantshaving a desired trait, such as a modulated level of low-nitrogentolerance. Selection and/or screening can be carried out over one ormore generations, and/or in more than one geographic location. In somecases, transgenic plants can be grown and selected under conditionswhich induce a desired phenotype or are otherwise necessary to produce adesired phenotype in a transgenic plant. In addition, selection and/orscreening can be applied during a particular developmental stage inwhich the phenotype is expected to be exhibited by the plant. Selectionand/or screening can be carried out to choose those transgenic plantshaving a statistically significant difference in low nitrogen tolerancelevel relative to a control plant that lacks the transgene. Selected orscreened transgenic plants have an altered phenotype as compared to acorresponding control plant, as described in the “Transgenic PlantPhenotypes” section herein.

C. Plant Species

The polynucleotides and vectors described herein can be used totransform a number of monocotyledonous and dicotyledonous plants andplant cell systems, including species from one of the followingfamilies: Acanthaceae, Alliaceae, Alstroemeriaceae, Amaryllidaceae,Apocynaceae, Arecaceae, Asteraceae, Berberidaceae, Bixaceae,Brassicaceae, Bromeliaceae, Cannabaceae, Caryophyllaceae,Cephalotaxaceae, Chenopodiaceae, Colchicaceae, Cucurbitaceae,Dioscoreaceae, Ephedraceae, Erythroxylaceae, Euphorbiaceae, Fabaceae,Lamiaceae, Linaceae, Lycopodiaceae, Malvaceae, Melanthiaceae, Musaceae,Myrtaceae, Nyssaceae, Papaveraceae, Pinaceae, Plantaginaceae, Poaceae,Rosaceae, Rubiaceae, Salicaceae, Sapindaceae, Solanaceae, Taxaceae,Theaceae, or Vitaceae.

Suitable species may include members of the genus Abelmoschus, Abies,Acer, Agrostis, Allium, Alstroemeria, Ananas, Andrographis, Andropogon,Artemisia, Arundo, Atropa, Berberis, Beta, Bixa, Brassica, Calendula,Camellia, Camptotheca, Cannabis, Capsicum, Carthamus, Catharanthus,Cephalotaxus, Chrysanthemum, Cinchona, Citrullus, Coffea, Colchicum,Coleus, Cucumis, Cucurbita, Cynodon, Datura, Dianthus, Digitalis,Dioscorea, Elaeis, Ephedra, Erianthus, Erythroxylum, Eucalyptus,Festuca, Fragaria, Galanthus, Glycine, Gossypium, Helianthus, Hevea,Hordeum, Hyoscyamus, Jatropha, Lactuca, Linum, Lolium, Lupinus,Lycopersicon, Lycopodium, Manihot, Medicago, Mentha, Miscanthus, Musa,Nicotiana, Oryza, Panicum, Papaver, Parthenium, Pennisetum, Petunia,Phalaris, Phleum, Pinus, Poa, Poinsettia, Populus, Rauwolfia, Ricinus,Rosa, Saccharum, Salix, Sanguinaria, Scopolia, Secale, Solanum, Sorghum,Spartina, Spinacea, Tanacetum, Taxus, Theobroma, Triticosecale,Triticum, Uniola, Veratrum, Vinca, Vitis, and Zea.

Suitable species include Panicum spp. or hybrid thereof, Sorghum spp. orhybrid thereof, sudangrass, Miscanthus spp. or hybrid thereof, Saccharumspp. or hybrid thereof, Erianthus spp., Populus spp., Andropogongerardii (big bluestem), Pennisetum purpureum (elephant grass)) orhybrid thereof (e.g., Pennisetum purpureum×Pennisetum typhoidum),Phalaris arundinacea (reed canarygrass), Cynodon dactylon(bermudagrass), Festuca arundinacea (tall fescue), Spartina pectinata(prairie cord-grass), Medicago sativa (alfalfa), Arundo donax (giantreed) or hybrid thereof, Secale cereale (rye), Salix spp. (willow),Eucalyptus spp. (eucalyptus), Triticosecale (triticum—wheat×rye),Tripsicum dactyloides (Eastern gammagrass), Leymus cinereus (basinwildrye), Leymus condensatus (giant wildrye) and bamboo.

In some embodiments, a suitable species can be a wild, weedy, orcultivated sorghum species such as, but not limited to, Sorghum almum,Sorghum amplum, Sorghum angustum, Sorghum arundinaceum, Sorghum bicolor(such as bicolor, guinea, caudatum, kafir, and durra), Sorghumbrachypodum, Sorghum bulbosum, Sorghum burmahicum, Sorghum controversum,Sorghum drummondii, Sorghum ecarinatum, Sorghum exstans, Sorghum grande,Sorghum halepense, Sorghum interjectum, Sorghum intrans, Sorghumlaxiflorum, Sorghum leiocladum, Sorghum macrospermum, Sorghummatarankense, Sorghum miliaceum, Sorghum nigrum, Sorghum nitidum,Sorghum plumosum, Sorghum propinquum, Sorghum purpureosericeum, Sorghumstipoideum, Sorghum sudanensese, Sorghum timorense, Sorghumtrichocladum, Sorghum versicolor, Sorghum virgatum, Sorghum vulgare, orhybrids such as Sorghum×almum, Sorghum×sudangrass or Sorghum×drummondii.

Suitable species also include Helianthus annuus (sunflower), Carthamustinctorius (safflower), Jatropha curcas (jatropha), Ricinus communis(castor), Elaeis guineensis (palm), Linum usitatissimum (flax), andBrassica juncea.

Suitable species also include Beta vulgaris (sugarbeet), and Manihotesculenta (cassava).

Suitable species also include Lycopersicon esculentum (tomato), Lactucasativa (lettuce), Musa paradisiaca (banana), Solanum tuberosum (potato),Brassica oleracea (broccoli, cauliflower, Brussels sprouts), Camelliasinensis (tea), Fragaria ananassa (strawberry), Theobroma cacao (cocoa),Coffea arabica (coffee), Vitis vinifera (grape), Ananas comosus(pineapple), Capsicum annum (hot & sweet pepper), Allium cepa (onion),Cucumis melo (melon), Cucumis sativus (cucumber), Cucurbita maxima(squash), Cucurbita moschata (squash), Spinacea oleracea (spinach),Citrullus lanatus (watermelon), Abelmoschus esculentus (okra), andSolanum melongena (eggplant).

Suitable species also include Papaver somniferum (opium poppy), Papaverorientale, Taxus baccata, Taxus brevifolia, Artemisia annua, Cannabissativa, Camptotheca acuminate, Catharanthus roseus, Vinca rosea,Cinchona officinalis, Colchicum autumnale, Veratrum californica,Digitalis lanata, Digitalis purpurea, Dioscorea spp., Andrographispaniculata, Atropa belladonna, Datura stomonium, Berberis spp.,Cephalotaxus spp., Ephedra sinica, Ephedra spp., Erythroxylum coca,Galanthus wornorii, Scopolia spp., Lycopodium serratum (=Huperziaserrata), Lycopodium spp., Rauwolfia serpentina, Rauwolfia spp.,Sanguinaria canadensis, Hyoscyamus spp., Calendula officinalis,Chrysanthemum parthenium, Coleus forskohlii, and Tanacetum parthenium.

Suitable species also include Parthenium argentatum (guayule), Heveaspp. (rubber), Mentha spicata (mint), Mentha piperita (mint), Bixaorellana, and Alstroemeria spp.

Suitable species also include Rosa spp. (rose), Dianthus caryophyllus(carnation), Petunia spp. (petunia) and Poinsettia pulcherrima(poinsettia).

Suitable species also include Nicotiana tabacum (tobacco), Lupinus albus(lupin), Uniola paniculata (oats), bentgrass (Agrostis spp.), Populustremuloides (aspen), Pinus spp. (pine), Abies spp. (fir), Acer spp.(maple), Hordeum vulgare (barley), Poa pratensis (bluegrass), Loliumspp. (ryegrass) and Phleum pratense (timothy).

Thus, the methods and compositions can be used over a broad range ofplant species, including species from the dicot genera Brassica,Carthamus, Glycine, Gossypium, Helianthus, Jatropha, Parthenium,Populus, and Ricinus; and the monocot genera Elaeis, Festuca, Hordeum,Lolium, Oryza, Panicum, Pennisetum, Phleum, Poa, Saccharum, Secale,Sorghum, Triticosecale, Triticum, and Zea. In some embodiments, a plantis a member of the species Panicum virgatum (switchgrass), Sorghumbicolor (sorghum, sudangrass), Miscanthus giganteus (miscanthus),Saccharum sp. (energycane), Populus balsamifera (poplar), Zea mays(corn), Glycine max (soybean), Brassica napus (canola), Triticumaestivum (wheat), Gossypium hirsutum (cotton), Oryza sativa (rice),Helianthus annuus (sunflower), Medicago sativa (alfalfa), Beta vulgaris(sugarbeet), or Pennisetum glaucum (pearl millet).

In certain embodiments, the polynucleotides and vectors described hereincan be used to transform a number of monocotyledonous and dicotyledenousplants and plant cell systems, wherein such plants are hybrids ofdifferent species or varieties of a specific species (e.g., Saccharumsp.×Miscanthus sp., Panicum virgatum×Panicum amarum, Panicumvirgatum×Panicum amarulum, and Pennisetum purpureum×Pennisetumtyphoidum).

D. Transgenic Plant Phenotypes

In some embodiments, a plant in which expression of a low nitrogentolerance-modulating polypeptide is modulated can have increased levelsof photosynthetic efficiency in seedlings. For example, a low nitrogentolerance-modulating polypeptide described herein can be expressed in atransgenic plant, resulting in increased levels of photosyntheticefficiency in growth conditions with low nitrogen sources. The level ofphotosynthetic efficiency can be increased by at least 0.25 percent,e.g., 0.25, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, or more than 60 percent, ascompared to the level of photosynthetic efficiency in a correspondingcontrol plant that does not express the transgene. In some embodiments,a plant in which expression of a low nitrogen tolerance-modulatingpolypeptide is modulated can have decreased levels of photosyntheticefficiency. The level of photosynthetic efficiency can be decreased byat least 0.25 percent, e.g., 0.25, 1, 2, 3, 4, 5, 10, 15, 20, 25, 30,35, or more than 35 percent, as compared to the level of photosyntheticin a corresponding control plant that does not express the transgene.

In some embodiments, a plant in which expression of a low nitrogentolerance-modulating polypeptide is modulated can have increased ordecreased levels of photosynthetic efficiency in one or more greentissues, e.g., leaves, stems, bulbs, flowers, fruits, young seeds. Forexample, the level of photosynthetic efficiency can be increased by atleast 0.25 percent, e.g., 0.25, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, or morethan 60 percent, as compared to the level of photosynthetic efficiencyin a corresponding control plant that does not express the transgene. Insome embodiments, a plant in which expression of a low nitrogentolerance-modulating polypeptide is modulated can have decreased levelsof photosynthetic efficiency in one or more green tissues. The level ofphotosynthetic efficiency can be decreased by at least 0.25 percent,e.g., 0.25, 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, or more than 35percent, as compared to the level of photosynthetic efficiency in acorresponding control plant that does not express the transgene.

Increases in photosynthetic efficiency in low-nitrogen growth conditionsin such plants can provide improved plant growth in geographic localeswhere plant's intake of nitrogenous fertilizers is often insufficient.Decreases in photosynthetic efficiency, and hence less tolerance tolow-nitrogen growth conditions in such plants can be useful for removingweeds and such from the environment, by applying to weeds and such. Forexample, a plant capable of inducing the decrease in photosyntheticefficiency can be prepared to apply for land improvements and such.

Typically, a difference in the level of photosynthetic efficiency in atransgenic plant or cell relative to a control plant or cell isconsidered statistically significant at p≦0.05 with an appropriateparametric or non-parametric statistic, e.g., Chi-square test, Student'st-test, Mann-Whitney test, or F-test. In some embodiments, a differencein the level of photosynthetic is statistically significant at p<0.01,p<0.005, or p<0.001. A statistically significant difference in, forexample, the level of photosynthetic efficiency in a transgenic plantcompared to the amount in cells of a control plant indicates that therecombinant nucleic acid present in the transgenic plant results inaltered levels of photosynthetic efficiency.

In some embodiments, a plant in which expression of a low nitrogentolerance-modulating polypeptide is modulated can have increased growthrates in seedlings. For example, a low nitrogen tolerance-modulatingpolypeptide described herein can be expressed in a transgenic plant,resulting in increased growth rate in growth conditions of limitingnitrogen sources. The growth rate can be increased by at least 2percent, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 25, 30, 35, 40, 45, 50, 55, 60, or more than 60 percent, ascompared to the growth rate in a corresponding control plant that doesnot express the transgene. In some embodiments, a plant in whichexpression of a low nitrogen tolerance-modulating polypeptide ismodulated can have decreased growth rates. The growth rate can bedecreased by at least 2 percent, e.g., 2, 3, 4, 5, 10, 15, 20, 25, 30,35, or more than 35 percent, as compared to the growth rate in acorresponding control plant that does not express the transgene. Growthrate can be measured in seedlings, developing, or mature plants andmeasured for periods of time such as about 1 hour, 3 hours, 6 hours, 12hours, 1 day, 3 days, 5 days, 10 days, 1 month, 3 months, 6 months, 12months, or the entire lifespan of a plant.

In some embodiments, a plant in which expression of a low nitrogentolerance-modulating polypeptide is modulated can have increased ordecreased growth rates in one or more vegetative and reproductivetissues, e.g., leaves, stems, flowers, bulbs, fruits, young seeds. Forexample, the growth rate can be increased by at least 2 percent, e.g.,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25,30, 35, 40, 45, 50, 55, 60, or more than 60 percent, as compared to thegrowth rate in a corresponding control plant that does not express thetransgene. In some embodiments, a plant in which expression of a lownitrogen tolerance-modulating polypeptide is modulated can havedecreased levels of growth rate in one or more vegetative tissues. Thegrowth rate can be decreased by at least 2 percent, e.g., 2, 3, 4, 5,10, 15, 20, 25, 30, 35, or more than 35 percent, as compared to thegrowth rate in a corresponding control plant that does not express thetransgene.

Increases in growth rate in low-nitrogen conditions in such plants canprovide improved plant growth and initial establishment in geographiclocales where plant's intake of nitrogenous fertilizers is ofteninsufficient. Decreases in growth rate, and hence less tolerance tolow-nitrogen growth conditions in such plants can be useful forengineering slow-growing plants, by applying to ornamentals and such.For example, a plant capable of inducing the decrease in growth rate canbe prepared to apply for land improvements and such.

Typically, a difference in the growth rate of a transgenic plant or cellrelative to a control plant or cell is considered statisticallysignificant at p≦0.05 with an appropriate parametric or non-parametricstatistic, e.g., Chi-square test, Student's t-test, Mann-Whitney test,or F-test. In some embodiments, a difference in the growth rate isstatistically significant at p<0.01, p<0.005, or p<0.001. Astatistically significant difference in, for example, the growth rate ofa transgenic plant compared to the growth rate of a control plantindicates that the recombinant nucleic acid present in the transgenicplant results in altered growth rates.

The phenotype of a transgenic plant is evaluated relative to a controlplant. A plant is said “not to express” a polypeptide when the plantexhibits less than 10%, e.g., less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%,1%, 0.5%, 0.1%, 0.01%, or 0.001%, of the amount of polypeptide or mRNAencoding the polypeptide exhibited by the plant of interest. Expressioncan be evaluated using methods including, for example, RT-PCR, Northernblots, S1 RNase protection, primer extensions, Western blots, proteingel electrophoresis, immunoprecipitation, enzyme-linked immunoassays,chip assays, and mass spectrometry. It should be noted that if apolypeptide is expressed under the control of a tissue-preferential orbroadly expressing promoter, expression can be evaluated in the entireplant or in a selected tissue. Similarly, if a polypeptide is expressedat a particular time, e.g., at a particular time in development or uponinduction, expression can be evaluated selectively at a desired timeperiod.

V. PLANT BREEDING

Genetic polymorphisms are discrete allelic sequence differences in apopulation. Typically, an allele that is present at 1% or greater isconsidered to be a genetic polymorphism. The discovery that polypeptidesdisclosed herein can modulate photosynthetic efficiency and/or nitrogencontent is useful in plant breeding, because genetic polymorphismsexhibiting a degree of linkage with loci for such polypeptides are morelikely to be correlated with variation in a low-nitrogen tolerancetrait. For example, genetic polymorphisms linked to the loci for suchpolypeptides are more likely to be useful in marker-assisted breedingprograms to create lines having a desired modulation in the low-nitrogentolerance trait.

Thus, one aspect of the invention includes methods of identifyingwhether one or more genetic polymorphisms are associated with variationin a low-nitrogen tolerance trait. Such methods involve determiningwhether genetic polymorphisms in a given population exhibit linkage withthe locus for one of the polypeptides depicted in FIGS. 1-57, SEQ IDNO:556, SEQ ID NO:853, SEQ ID NO:1157 and/or a functional homologthereof, such as, but not limited to those identified in the SequenceListing of this application. The correlation is measured betweenvariation in the low-nitrogen tolerance trait in plants of thepopulation and the presence of the genetic polymorphism(s) in plants ofthe population, thereby identifying whether or not the geneticpolymorphism(s) are associated with variation for the trait. If thepresence of a particular allele is statistically significantlycorrelated with a desired modulation in the low-nitrogen tolerancetrait, the allele is associated with variation for the trait and isuseful as a marker for the trait. If, on the other hand, the presence ofa particular allele is not significantly correlated with the desiredmodulation, the allele is not associated with variation for the traitand is not useful as a marker.

Such methods are applicable to populations containing the naturallyoccurring endogenous polypeptide rather than an exogenous nucleic acidencoding the polypeptide, i.e., populations that are not transgenic forthe exogenous nucleic acid. It will be appreciated, however, thatpopulations suitable for use in the methods may contain a transgene foranother, different trait, e.g., herbicide resistance.

Genetic polymorphisms that are useful in such methods include simplesequence repeats (SSRs, or microsatellites), rapid amplification ofpolymorphic DNA (RAPDs), single nucleotide polymorphisms (SNPs),amplified fragment length polymorphisms (AFLPs) and restriction fragmentlength polymorphisms (RFLPs). SSR polymorphisms can be identified, forexample, by making sequence specific probes and amplifying template DNAfrom individuals in the population of interest by PCR. If the probesflank an SSR in the population, PCR products of different sizes will beproduced. See, e.g., U.S. Pat. No. 5,766,847. Alternatively, SSRpolymorphisms can be identified by using PCR product(s) as a probeagainst Southern blots from different individuals in the population.See, U. H. Refseth et al. (1997) Electrophoresis 18: 1519. Theidentification of RFLPs is discussed, for example, in Alonso-Blanco etal. (Methods in Molecular Biology, vol. 82, “Arabidopsis Protocols”, pp.137-146, J. M. Martinez-Zapater and J. Salinas, eds., c. 1998 by HumanaPress, Totowa, N.J.); Burr (“Mapping Genes with Recombinant Inbreds”,pp. 249-254, in Freeling, M. and V. Walbot (Ed.), The Maize Handbook, c.1994 by Springer-Verlag New York, Inc.: New York, N.Y., USA; BerlinGermany; Burr et al. (1998) Genetics 118: 519; and Gardiner, J. et al.(1993) Genetics 134: 917). The identification of AFLPs is discussed, forexample, in EP 0 534 858 and U.S. Pat. No. 5,878,215.

In some embodiments, the methods are directed to breeding a plant line.Such methods use genetic polymorphisms identified as described above ina marker assisted breeding program to facilitate the development oflines that have a desired alteration in the low-nitrogen tolerancetrait. Once a suitable genetic polymorphism is identified as beingassociated with variation for the trait, one or more individual plantsare identified that possess the polymorphic allele correlated with thedesired variation. Those plants are then used in a breeding program tocombine the polymorphic allele with a plurality of other alleles atother loci that are correlated with the desired variation. Techniquessuitable for use in a plant breeding program are known in the art andinclude, without limitation, backcrossing, mass selection, pedigreebreeding, bulk selection, crossing to another population and recurrentselection. These techniques can be used alone or in combination with oneor more other techniques in a breeding program. Thus, each identifiedplants is selfed or crossed a different plant to produce seed which isthen germinated to form progeny plants. At least one such progeny plantis then selfed or crossed with a different plant to form a subsequentprogeny generation. The breeding program can repeat the steps of selfingor outcrossing for an additional 0 to 5 generations as appropriate inorder to achieve the desired uniformity and stability in the resultingplant line, which retains the polymorphic allele. In most breedingprograms, analysis for the particular polymorphic allele will be carriedout in each generation, although analysis can be carried out inalternate generations if desired.

In some cases, selection for other useful traits is also carried out,e.g., selection for fungal resistance or bacterial resistance. Selectionfor such other traits can be carried out before, during or afteridentification of individual plants that possess the desired polymorphicallele.

VI. ARTICLES OF MANUFACTURE

Transgenic plants provided herein have various uses in the agriculturaland energy production industries. For example, transgenic plantsdescribed herein can be used to make animal feed and food products. Suchplants, however, are often particularly useful as a feedstock for energyproduction. Transgenic plants described herein often produce higheryields of grain and/or biomass per hectare, relative to control plantsthat lack the exogenous nucleic acid. In some embodiments, suchtransgenic plants provide equivalent or even increased yields of grainand/or biomass per hectare relative to control plants when grown underconditions of reduced inputs such as fertilizer and/or water. Thus, suchtransgenic plants can be used to provide yield stability at a lowerinput cost and/or under environmentally stressful conditions such asdrought or limiting nitrogen sources. In some embodiments, plantsdescribed herein have a composition that permits more efficientprocessing into free sugars, and subsequently ethanol, for energyproduction. In some embodiments, such plants provide higher yields ofethanol, butanol, dimethyl ether, other biofuel molecules, and/orsugar-derived co-products per kilogram of plant material, relative tocontrol plants. Such processing efficiencies are believed to be derivedfrom the nitrogenous composition of the plant material. By providinghigher yields at an equivalent or even decreased cost of production, thetransgenic plants described herein improve profitability for farmers andprocessors as well as decrease costs to consumers.

Seeds from transgenic plants described herein can be conditioned andbagged in packaging material by means known in the art to form anarticle of manufacture. Packaging material such as paper and cloth arewell known in the art. A package of seed can have a label, e.g., a tagor label secured to the packaging material, a label printed on thepackaging material, or a label inserted within the package, thatdescribes the nature of the seeds therein.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

VII. EXAMPLES Example 1 Transgenic Arabidopsis Plants

The following symbols are used in the Examples with respect toArabidopsis transformation: T₁: first generation transformant; T₂:second generation, progeny of self-pollinated T₁ plants; T₃: thirdgeneration, progeny of self-pollinated T₂ plants; T₄: fourth generation,progeny of self-pollinated T₃ plants. Independent transformations arereferred to as events.

The following is a list of nucleic acids that were isolated fromArabidopsis thaliana plants, CeresClone:29661 (SEQ ID NO:1),CeresClone:251343 (SEQ ID NO:48), CeresClone:19586 (SEQ ID NO:76),CeresClone:25136 (SEQ ID NO:96), CeresClone:1820 (SEQ ID NO:99),CeresClone:13102 (SEQ ID NO:151), CeresClone:15457 (SEQ ID NO:165),Ceres Annot:859276 (SEQ ID NO:175), CeresClone:17883 (SEQ ID NO:185),CeresClone:251590 (SEQ ID NO:207), CeresClone:4898 (SEQ ID NO:217),CeresClone:148977 (SEQ ID NO:233), CeresClone:24255 (SEQ ID NO:245),CeresClone:38432 (SEQ ID NO:299), Ceres Annot:553243 (SEQ ID NO:331),CeresClone:1011900 (SEQ ID NO:367), CeresClone:5232 (SEQ ID NO:509),CeresClone:29302 (SEQ ID NO:532), CeresClone:93971 (SEQ ID NO:555),Ceres Annot:12669619_cDNA (SEQ ID NO:557), CeresClone:21608 (SEQ IDNO:592), CeresClone:2031 (SEQ ID NO:612), CeresClone:94503 (SEQ IDNO:645), CeresClone:21740 (SEQ ID NO:686), CeresClone:5609 (SEQ IDNO:729), CeresClone:3137 (SEQ ID NO:745), CeresClone:32430 (SEQ IDNO:768), CeresClone:101255 (SEQ ID NO:791), Ceres Annot:573161 (SEQ IDNO:854), Ceres Annot:552727 (SEQ ID NO:890), CeresClone:732 (SEQ IDNO:1193), CeresClone:2267 (SEQ ID NO:1209), CeresClone:39358 (SEQ IDNO:1273), CeresClone:115046 (SEQ ID NO:1301), Ceres Annot:850581 (SEQ IDNO:1427), Ceres Annot:862321 (SEQ ID NO:1462), Ceres Annot:839064 (SEQID NO:1478), Ceres Annot:864666 (SEQ ID NO:1490), Ceres Annot:875012(SEQ ID NO:1509), Ceres Annot:874016 (SEQ ID NO:1524), CeresAnnot:827304 (SEQ ID NO:1536), Ceres Annot:869192 (SEQ ID NO:1553), andCeres Annot:876419 (SEQ ID NO:1576). The nucleic acid designated CeresClone: 968180 (SEQ ID NO:1115) was isolated from the species Brassicanapus. The nucleic acid designated Ceres Clone: 1017441 (SEQ ID NO:224)was isolated from the species Triticum aesticum. The following is a listof nucleic acids that were isolated from Zea mays plants,CeresClone:1387146 (SEQ ID NO:981), CeresClone:1408950 (SEQ ID NO:1098,CeresClone:208453 (SEQ ID NO:1111), CeresClone:208995 (SEQ ID NO:943),CeresClone:225681 (SEQ ID NO:975), CeresClone:239806 (SEQ ID NO:916),CeresClone:244306 (SEQ ID NO:1053), CeresClone:276809 (SEQ ID NO:823),CeresClone:324216 (SEQ ID NO:852), CeresClone:339439 (SEQ ID NO:1341),CeresClone:424522 (SEQ ID NO:827), CeresClone:896483 (SEQ ID NO:1384),CeresClone:986438 (SEQ ID NO:1156), CeresClone:988083 (SEQ ID NO:1184),CeresClone:995409 (SEQ ID NO:1408), CeresClone:996227 (SEQ ID NO:1158),and CeresClone:996263 (SEQ ID NO:1165).

With the exception of Ceres Clone:29661 (SEQ ID NO:1), each isolatednucleic acid described above was cloned into a Ti plasmid vector,CRS338, containing a phosphinothricin acetyltransferase gene whichconfers FINALE™ resistance to transformed plants. Constructs were madeusing CRS338 that contained SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96,SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ IDNO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532,SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ IDNO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854,SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ IDNO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115,SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ IDNO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341,SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ IDNO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553,or SEQ ID NO:1576, each operably linked to a 35S promoter. CeresClone:29661 (SEQ ID NO:1) was cloned into a Ti plasmid vector, CRS 311,containing a phosphinothricin acetyltransferase gene, which confersFINALE™ resistance to transformed plants. SEQ ID NO:1 was operablylinked to a p32449 promoter in the constructs made using the CRS 331vector. Wild-type Arabidopsis thaliana ecotype Wassilewskija (Ws) plantswere transformed separately with each construct. The transformationswere performed essentially as described in Bechtold et al. (1993) C.R.Acad. Sci. Paris, 316:1194-1199.

Transgenic Arabidopsis lines containing SEQ ID NO:1, SEQ ID NO:48, SEQID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245,SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ IDNO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768,SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ IDNO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQID NO:981, SEQ ID NO:224, SEQ ID NO:1053, SEQ ID NO:1098, SEQ IDNO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165,SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ IDNO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427,SEQ ID NO:1462, SEQ ID NO:1478, SEQ ID NO:1490, SEQ ID NO:1509, SEQ IDNO:1524, SEQ ID NO:1536, SEQ ID NO:1553, SEQ ID NO:1576, or SEQ IDNO:175 were designated ME00919, ME01312, ME01463, ME01821, ME01910,ME02538, ME02603, ME02613, ME02801, ME03123, ME04204, ME04477, ME04507,ME04587, ME04753, ME04772, ME04909, ME05033, ME05194, ME05267, ME05300,ME05341, ME05392, ME05429, ME05493, ME05885, ME07344, ME07859, ME08464,ME09939, ME11735, ME12910, ME12927, ME12929, ME12954, ME12970, ME13006,ME13021, ME13064, ME13071, ME13087, ME13106, ME13107, ME13108, ME13110,ME13125, ME13149, ME13151, ME13153, ME13177, ME13200, ME13204, ME14649,ME16546, ME17457, ME17567, ME17932, ME17936, ME18275, ME18924, ME19182,or ME20628, respectively. The presence of each vector containing anucleic acid described above in the respective transgenic Arabidopsisline transformed with the vector was confirmed by FINALE™ resistance,PCR amplification from green leaf tissue extract, and/or sequencing ofPCR products. As controls, wild-type Arabidopsis ecotype Ws plants weretransformed with the empty vector, either CRS338 or CRS311.

Example 2 Screening for Transgenic Plants Tolerant to Low-NitrogenGrowth Conditions

A low-nitrogen tolerance screen was carried out on seedlings in order toidentify transgenic lines that showed increased photosynthesisefficiency or seedling size or greenness under limiting nitrogenconditions relative to the internal control plants. The media used forthe low-nitrogen tolerance assay contained 0.5% sucrose, 0.5×MS withoutnitrogen media (PhytoTech), 0.05% MES Hydrate, and 0.8% Phytagar. Inaddition, for low ammonium nitrate assay, 240 μM NH4NO3 was used asnitrogen source. For low nitrate assay, nitrogen source was 300 μM KNO3.pH of the media was adjusted to pH 5.7 using 10N KOH. Sterilized seedswere plated on agar plates and stratified for 2 days in the dark at 4°C. to promote uniform germination. Agar plates with germinatingseedlings were placed horizontally in a CONVIRON® growth chamber set at22° C., 16:8 hour light:dark cycle, 70% humidity with a combination ofincandescent and fluorescent lamps emitting a light intensity of ˜100μEinsteins. The control plates were placed randomly within the set.Screen the seedlings daily starting at 14 days. In this screen,seedlings that were larger or greener relative to the internal controlson low nitrogen growth media were selected. As they were found each day,candidate seedlings were aseptically transplanted to standard MSgermination plates for recovery. This intermediate recovery step wasnecessary before transplanting to soil to minimize the overall candidatemortality rate. The scoring and transplanting of candidates werecontinued until all remaining plants were small and yellowed fromnitrogen stress. On the very last day of scoring, each plate was scannedfor photosynthetic efficiency (Fv/Fm) on the chlorophyll fluorescence(CF) imager and scored as candidates and transplanted any extremeoutliers on the high end of Fv/Fm scores. Fv/Fm ratio typically providesan estimate of the photosystem II (PSII) maximum efficiency withindark-adapted material where Fv is variable fluorescence, i.e. differencebetween minimum (Fo) and maximum (Fm) fluorescence signal, fromdark-adapted material. This could be done visually by looking at thefalse color image for each seedling using the CF image analysis software(plants with high end Fv/Fm scores appear red). This step was typicallydone at ˜24 days after germination. Seven days after being transferredto MS recovery plates, candidates were transplanted to soil (standardSunshine:vermiculite 3:2 mix; Osmocote; Marathon). Five days after beingtransplanted to soil, candidates were sprayed with FINALE® [5 mLFINALE®/48 oz. water] to eliminate non-transgenics from the population.Two days after spraying with FINALE®, cauline leaf tissue of eachcandidate was collected for genomic DNA extraction, PCR, and sequencingto determine the identity of the transgene for each candidate.

Example 3 Validation Plate Assay

This assay was designed to validate transgenic lines that showedincreased photosynthesis or size under limiting nitrogen conditionsrelative to the internal control. The media used for the low-nitrogentolerance assay contained 0.5% sucrose, 0.5×MS without nitrogen media(PhytoTech), 0.05% MES Hydrate, and 0.8% Phytagar. pH of the media wasadjusted to pH 5.7 using 10N KOH. In addition, for low ammonium nitrateassay, 240 μM NH₄NO₃ was used as nitrogen source. For low nitrate assay,nitrogen source was 300 μM KNO₃. Sterilized seeds were plated on agarplates and stratified for 2 days in the dark at 4° C. to promote uniformgermination. Agar plates with germinating seedlings were placedhorizontally in a CONVIRON® growth chamber set at 22° C., 16:8 hourlight:dark cycle, 70% humidity with a combination of incandescent andfluorescent lamps emitting a light intensity of ˜100 μEinsteins. Thecontrol plates were placed randomly within the set. Plates were scannedevery other day using the CF Imager (after 45 minute ofdark-acclimation) and were completed after all wild-type plants havecompletely yellowed. After the plates were scanned on the last day, theywere sprayed with FINALE® (10 mL FINALE® into 48 oz. full-strength MSliquid media). Two days after spraying, each plate was dark-acclimatedfor 45 minutes and scanned for Fv/Fm on the CF imager and scored foreach of the plants at each time point. For each separate time point, thedata for all the T₂ transgenic plants across an event was pooled and aone-tailed t-test was used to compare both the Fv/Fm ratios and rosetteareas relative to the pooled non-transgenics across the same plate.Whenever possible, this process was repeated for the T₃ generationplants. A low nitrogen tolerant candidate was confirmed when thetransgenic Fv/Fm ratio and/or rosette area was greater than thewild-type segregants with a p-value≦0.05 in 2 or more events in bothgenerations

Example 4 Validation Soil Assay

A Low, Medium, and High Nitrogen experiment on soil was carried out toassess phenotypic characteristics at a mature point in the life cycle ofArabidopsis, as compared to seedling screens. The lines to be testedwere originally identified through superpool screens for low nitrate andlow ammonium nitrate tolerance. These lines were later individuallyassayed as seedlings on low nitrate and low ammonium nitrate agar. Forthis assay, MetroMix200 soil was mixed with vermiculite and Marathon™(MetroMix200:vermiculite 3:2 mix; Osmocote; Marathon) autoclaved andcooled before use. Experimental plants and controls were randomizedacross the flats. Prior to sowing seed, each flat was watered with 3 Lfiltered water. Flats with 24 wells were filled with the following 3:2ratios of MetroMix200 to Thermorock vermiculite. At the beginning of theexperiment no nitrogen was provided until 2 weeks after germination when¼ Hoaglands supplemented with KNO₃ at 25 ppm, 250 ppm, and 1500 ppm wereused to water the flats from beneath.

Seeds were stratified on soil and in the dark at 4° C. for 3 days. Afterthe cold treatment, flats were transferred to the growth chamber. Plantswere grown for approximately 5 weeks, or until full grown/mature. Plantswere then dark-acclimated for one hour. Chlorophyll fluorescence imageswere taken using a CF-Imager (Technologica, UK) according to themanufacturer's protocol to measure the performance and efficiency ofphotosystem II: 1) Fv/Fm, maximum photosystem II efficiency 2) Fq′/Fm′,operating efficiency and 3) non-photochemical quenching (NPQ).

One week after watering with ¼ Hoaglands supplemented with various KNO₃concentrations, plant rosette area measurements were taken using theWhinRhizo imaging software (Reagent Instruments, Canada). The plantswere then collected in manila envelopes, placed in a 125° C. drying ovenfor 1-2 days and weighed

Example 5 Analysis of ME00919 Events

ME00919 contains Ceres Clone:29661 (At3g61880, SEQ ID NO:1) fromArabidopsis thaliana, which encodes a 534 amino acid cytochrome P450protein. Evaluation of low-nitrogen tolerance for ME00919 in T₂ and T₃was conducted under the same conditions as described in Example 2. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -01 and -03, showedsignificantly increased photosynthetic efficiency relative to theinternal controls in both generations at p≦0.05 using a one-tailedt-test assuming unequal variance. A summary of photosynthetic efficiencyof ME00919 seedlings on low ammonium nitrate-containing media are shownin Table 1. Events -01 and -03 segregated 15:1 and 3:1 (R:S),respectively, for FINALE™ resistance in the T₂ generation. ME00919events were also tested for enhanced growth on the low ammonium nitratemedia. No significant differences between the transgenics and thecontrols were observed.

TABLE 1 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME00919 ME00919-01 0.6564130446 0.595818 11 2.48 × 10⁻² (T₂) ME00919 ME00919-01 0.66348780 410.595818 11 1.55 × 10⁻² (T₃) ME00919 ME00919-03 0.67212195 41 0.63402638 3.35 × 10⁻³ (T₂) ME00919 ME00919-03 0.69278947 19 0.634026 38 2.39 ×10⁻⁵ (T₃)

Events -01 and -03 of ME00919 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 6 Analysis of ME01312 Events

ME01312 contains Ceres Clone:251343 (At3g21270, SEQ ID NO:48) fromArabidopsis thaliana, which encodes a 204 amino acid Dof zinc fingerprotein. Ceres Clone:251343 shares approximately 40% amino acid identityto the corn Dof1 gene, which when overexpressed in Arabidopsis, hasshown to confer tolerance to plants receiving low nitrogen stress(Yanagisawa et al., 2004). Evaluation of low-nitrogen tolerance forME01312 in T₂ and T₃ was conducted under the same conditions asdescribed in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -03 and -11, showed significantly enhancedphotosynthetic efficiency on either low nitrate or low ammoniumnitrate-containing media after 16 and 17 days compared to the internalcontrols in both generations at p≦0.05 using a one-tailed t-testassuming unequal variance. Event -03 had a slightly greater p-value than0.05 in the T₃ generation for the low nitrate screen, significant atp≦0.10. A summary of photosynthetic efficiency of ME01312 seedlings oneither low nitrate or low ammonium nitrate-containing media is shown inTable 2. Events -03 and -11 segregated 3:1 (R:S), respectively, forFINALE™ resistance in the T₂ generation.

TABLE 2A T-test comparison of photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 16 daysof growth on low nitrate. Pooled Non- Transgenic Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME01312 ME01312-03 (T₂) 0.63 38 0.60 580.03 ME01312 ME01312-03 (T₃) 0.63 38 0.60 58 0.07 ME01312 ME01312-11(T₂) 0.64 41 0.60 58 0.019 ME01312 ME01312-11 (T₃) 0.64 47 0.60 58 9.89× 10⁻³

TABLE 2B T-test comparison of photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 17 daysof growth on low ammonium nitrate Pooled Transgenic Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME01312 ME01312-03 (T₂) 0.6436 0.61 88 2.64 × 10⁻³ ME01312 ME01312-03 (T₃) 0.66 27 0.61 88 1.87 ×10⁻⁵ ME01312 ME01312-11 (T₂) 0.65 35 0.61 88 7.06 × 10⁻⁴ ME01312ME01312-11 (T₃) 0.64 37 0.61 88 0.011

Events -03-11 of ME01312 exhibited no statistically relevant negativephenotypes. That is, there was no detectable reduction in germinationrate, the transgenic plants appeared wild type in all instances; therewas no observable or statistical differences between transgenics andcontrols in days to flowering; there was no observable or statisticaldifferences between transgenics and controls in the size of the rosettearea 7 days post-bolting; and there was no observable or statisticaldifferences between transgenics and controls in fertility (siliquenumber and seed fill).

Example 7 Analysis of ME01463 Events

ME01463 contains Ceres Clone:19586 (At1g80600, SEQ ID NO:76) fromArabidopsis thaliana, which encodes a 457 acetylornithineaminotransferase, a member of the Class-III aminotransferase family.Evaluation of low-nitrogen tolerance for ME01463 in two generations wasconducted under the same conditions as described in Examples 2 and 3. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Three events, -02, -06, and -10, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate containing-media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME01463 seedlings isshown in Table 3. Events -02, -06, and -10 segregated 2:1, 2:1 and 3:1(R:S), respectively, for FINALE™ resistance in the T₂ generation.ME01463 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed (data not shown).

TABLE 3 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME01463 ME01463-02 (T₃)0.6815 26 0.6376 122 2.47 × 10⁻⁴ ME01463 ME01463-02 (T₄) 0.6701 410.6376 122 1.57 × 10⁻³ ME01463 ME01463-06 (T₃) 0.6615 31 0.6376 122 2.37× 10⁻² ME01463 ME01463-06 (T₄) 0.6881 35 0.6376 122 5.85 × 10⁻⁶ ME01463ME01463-10 (T₂) 0.6699 33 0.6376 122 2.25 × 10⁻³ ME01463 ME01463-10 (T₃)0.6809 18 0.6376 122 4.60 × 10⁻⁴

Events -02, -06, and -10 of ME01463 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 8 Analysis of ME01821 Events

ME01821 contains Ceres Clone:25136 (At1g65500, SEQ ID NO:96) fromArabidopsis thaliana, which encodes a 86 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME01821 in T₂generation was conducted under the same conditions as described inExamples 2 and 3. In this study, the seedling photosynthetic efficiencywas measured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Three events,-01, -04 and -05, showed significantly increased photosyntheticefficiency on low nitrate-containing media relative to the internalcontrols in T₂ generation. Two events, -04 and -05, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in T₂ generation at p≦0.05 usinga one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME01821 seedlings is shown in Table 4.

TABLE 4A T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Transgenic Non-Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME01821 ME01821-01 (T₂) 0.06745 15 0.652033 3.76 × 10⁻² ME01821 ME01821-04 (T₂) 0.6826 17 0.6614 14 2.76 × 10⁻²ME01821 ME01821-05 (T₂) 0.6826 20 0.6614 14 3.74 × 10⁻²

TABLE 4B T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Transgenic Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME01821 ME01821-04 (T₂)0.7422 13 0.7166 21 5.20 × 10⁻³ ME01821 ME01821-05 (T₂) 0.7426 19 0.716621 6.07 × 10⁻³

A summary of the enhanced growth of ME01812 events on either lownitrate- or low ammonium nitrate-containing media is shown in Table 5.For two events -01 and -05, transgenic seedlings were foundsignificantly larger than the pooled non-transgenic segregants after 14days of growth on low nitrate-containing media (Table 5A). Transgenicseedlings of two events -02 and -05 were found significantly larger thanthe pooled non-transgenic segregants after 14 days of growth on lowammonium nitrate-containing media (Table 5B). In this study, theseedling area for transgenic plants within an event was compared to theseedling area for non-transgenic segregants pooled across the same line.

TABLE 5A T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non- Transgenic Transgenics t-test Line Events Area nArea n p-value ME01821 ME01821-01 (T₂) 0.0608 15 0.0555 33 3.97 × 10⁻²ME01821 ME01821-05 (T₂) 0.0666 20 0.0530 14 3.05 × 10⁻⁶

TABLE 5B T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME01821 ME01821-02 (T₂) 0.0750 19 0.0567 21 8.94 ×10⁻⁵ ME01821 ME01821-05 (T₂) 0.0680 19 0.0567 21 7.89 × 10⁻³

Example 9 Analysis of ME01910 Events

ME01910 contains Ceres Clone:1820 (At2g30620, SEQ ID NO:99) fromArabidopsis thaliana, which encodes a 273 amino acid linker histone H1and H5 family protein. Evaluation of low-nitrogen tolerance for ME01910in T₂ and T₃ was conducted under the same conditions as described inExamples 2 and 3. In this study, the seedling photosynthetic efficiencywas measured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, -01and -02, showed significantly increased photosynthetic efficiencyrelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME01910 seedlings is shown in Table 6. Events -01 and -02segregated 3:1 (R:S) for FINALE™ resistance in the T₂ generation.ME01910 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 6 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME01910 ME01910-01 (T₂)0.60433 39 0.56396 27 2.03 × 10⁻² ME01910 ME01910-01 (T₃) 0.61274 310.56396 27 9.23 × 10⁻³ ME01910 ME01910-02 (T₂) 0.62705 37 0.58083 297.39 × 10⁻³ ME01910 ME01910-02 (T₃) 0.64146 24 0.58083 29 9.23 × 10⁻⁴

Events -01 and -02 of ME01910 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 10 Analysis of ME02538 Events

ME02538 contains Ceres Clone:13102 (At1g67920, SEQ ID NO:151) fromArabidopsis thaliana, which encodes a 67 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME02538 in T₂generation was conducted under the same conditions as described inExample 2. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, —04and -05, showed significantly increased photosynthetic efficiencyrelative to the internal controls in T₂ generation on both lownitrate-containing and ammonium nitrate-containing media at p≦0.05 usinga one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME01821 seedlings is shown in Table 7.

TABLE 7A T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Non- Transgenic Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME02538 ME02538-04 (T₂) 0.6686 15 0.617124 1.92 × 10⁻⁴ ME02538 ME02538-05 (T₂) 0.6420 20 0.6171 24 4.84 × 10⁻²

TABLE 7B T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME02538 ME02538-04 (T₂)0.7345 13 0.7080 22 4.45 × 10⁻³ ME02538 ME02538-05 (T₂) 0.7356 20 0.708022 5.93 × 10⁻³

ME02538 events were also tested for enhanced growth on the low ammoniumnitrate media. A summary of the growth assay performed on ME01812 eventsis shown in Table 8. Transgenic seedlings of two events -01 and -02 werefound significantly larger than the pooled non-transgenic segregants onboth low nitrate- (Table 8A) and low ammonium nitrate-containing media(Table 8B).

TABLE 8A T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non- Transgenic Transgenics t-test Line Events Area nArea n p-value ME02538 ME02538-01 (T₂) 0.0655 16 0.0558 36 2.80 × 10⁻⁴ME02538 ME02538-02 (T₂) 0.0651 13 0.0601 20 1.32 × 10⁻²

TABLE 8B T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME02538 ME02538-01 (T₂) 0.0856 15 0.0737 39 8.60 ×10⁻³ ME02538 ME02538-02 (T₂) 0.0864 14 0.0776 22 3.13 × 10⁻²

Example 11 Analysis of ME02603 Events

ME02603 contains Ceres Clone:15457 (At5g47610, SEQ ID NO:165) fromArabidopsis thaliana, which encodes a 166 amino acid zinc ion bindingprotein. Evaluation of low-nitrogen tolerance for ME02603 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -01 and -04, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME02603 seedlings isshown in Table 9. Events -01 and -04 segregated 3:1 (R:S) for FINALE™resistance in the T₂ generation. Transgenic plants of two events -01 and-04—were also tested for enhanced photosynthetic efficiency on the lownitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 9 T-test comparison of photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 17 days(21 days for the T₂ generation of ME02603-01) of growth on low ammoniumnitrate. Pooled Non- Transgenic Transgenics t-test Line Events Fv/Fm nFv/Fm n p-value ME02603 ME02603-01 (T₂) 0.61 10 0.54 32 9.00 × 10⁻⁴ME02603 ME02603-01 (T₃) 0.67 28 0.65 62 6.11 × 10⁻³ ME02603 ME02603-04(T₂) 0.69 25 0.65 62 4.45 × 10⁻⁵ ME02603 ME02603-04 (T₃) 0.68 24 0.65 627.53 × 10⁻³

Events -01 and -04 of ME02603 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 12 Analysis of ME02613 Events

ME02613 contains Ceres Clone:17883 (At3g13910, SEQ ID NO:185) fromArabidopsis thaliana, which encodes a 102 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME02613 in T₂generation was conducted under the same conditions as described inExamples 2 and 3. In this study, the seedling photosynthetic efficiencywas measured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. In T₂generation, two events, -01 and -04, showed significantly increasedphotosynthetic efficiency on low nitrate containing-media relative tothe internal controls in T₂ generation at p≦0.05 using a one-tailedt-test assuming unequal variance. Two events, -03 and -04, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate containing-media relative to the internal controls in T₂generation at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME02613 seedlings isshown in Table 10.

TABLE 10A T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after14 days of growth on low nitrate. Pooled Transgenic Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME02613 ME02613-01 (T₂)0.6979 16 0.6630 21 1.45 × 10⁻² ME02613 ME02613-04 (T₂) 0.7046 13 0.663021 5.73 × 10⁻⁴

TABLE 10B T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after18 days of growth on low ammonium nitrate. Pooled TransgenicNon-Transgenics t-test Line Events Fv/Fm n Fv/Fm n p-value ME02613ME02613-03 (T₂) 0.7270 9 0.7068 29 4.34 × 10⁻² ME02613 ME02613-04 (T₂)0.7485 15 0.7068 29 7.09 × 10⁻⁵

A summary of the enhanced growth of ME02613 events on either lownitrate- or low ammonium nitrate-containing media is shown in Table 11.For two events -01 and -03, transgenic seedlings were foundsignificantly larger than the pooled non-transgenic segregants after 14days of growth on low nitrate-containing media (Table 11A). Transgenicseedlings of two events -02 and -03 were found significantly larger thanthe pooled non-transgenic segregants after 14 days of growth on lowammonium nitrate-containing media (Table 11B).

TABLE 11A T-test comparison of seedling area between transgenicseedlings and pooled non-transgenic segregants after 14 days of growthon low nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME02613 ME02613-01 0.05706 16 0.05259 31 4.71 ×10⁻² (T₂) ME02613 ME02613-03 0.06236 12 0.05789 29 2.39 × 10⁻² (T₂)

TABLE 1 T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME02613 ME02613-02 0.08324 14 0.07018 29 2.72 ×10⁻⁴ (T₂) ME02613 ME02613-03 0.08273 9 0.07018 29 1.41 × 10⁻² (T₂)

Example 13 Analysis of ME02801 Events

ME02801 contains Ceres Clone:251590 (At3g53080, SEQ ID NO:207) fromArabidopsis thaliana, which encodes a 155 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME02801 in T₂ and T₃was conducted under the same conditions as described in Example 2 and 3.In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -02 and -04, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME02801 seedlings isshown in Table 12. Events -02 and -04 segregated 3:1 (R:S) for FINALE™resistance in the T₂ generation. ME02801 events were also tested forenhanced growth on the low nitrate media and enhanced photosyntheticefficiency and growth on low ammonium nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 12 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Non- Transgenic Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME02801 ME02801-02 0.536385 39 0.465903113 5.49 × 10⁻⁷ (T₂) ME02801 ME02801-02 0.536465 43 0.465903 113 5.11 ×10⁻⁷ (T₃) ME02801 ME02801-04 0.532419 31 0.465903 113 1.28 × 10⁻⁵ (T₂)ME02801 ME02801-04 0.510406 32 0.465903 113 1.74 × 10⁻² (T₃)

Events -02 and -04 of ME02801 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 14 Analysis of ME03123 Events

ME03123 contains Ceres Clone:4898 (At1g29970, SEQ ID NO:217) fromArabidopsis thaliana, which encodes a 158 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME03123 in T₂ and/orT₃ was conducted under the same conditions as described in Examples 2and 3. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. A summary ofphotosynthetic efficiency of ME03123 seedlings is shown in Table 13. Twoevents, -01 and -10, showed significantly increased photosyntheticefficiency on low nitrate- or low ammonium nitrate-containing mediarelative to the internal controls in T₂ or T₃ generation at p≦0.05 usinga one-tailed t-test assuming unequal variance.

TABLE 13A T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after14 days of growth on low nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME03123 ME03123-01 0.6282 150.5732 26 6.60 × 10⁻⁵ (T₂) ME03123 ME03123-10 0.6069 12 0.5732 26 1.05 ×10⁻² (T₃)

TABLE 13B T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after18 days of growth on low ammonium nitrate. Pooled Non- TransgenicTransgenics t-test Line Events Fv/Fm n Fv/Fm n p-value ME03123ME03123-01 0.6736 17 0.6315 16 1.74 × 10⁻² (T₂) ME03123 ME03123-100.6699 20 0.6315 16 1.60 × 10⁻² (T₃)

ME03123 events were also tested for enhanced growth on the low ammoniumnitrate media. In this assay, transgenic seedlings of ME03123-02 andME03123-04 (T₂) were significantly larger than the pooled non-transgenicsegregants after 14 days of growth on low nitrate (Table 14).

TABLE 14 T-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non- Transgenic Transgenics t-test Line Events Area nArea n p-value ME03123 ME03123-02 (T₂) 0.07235 19 0.05623 20 1.41 × 10⁻⁶ME03123 ME03123-04 (T₃) 0.06571 7 0.05729 41 7.74 × 10⁻³

Example 15 Analysis of ME04204 Events

ME04204 contains Ceres Clone:148977 (At1g78770, SEQ ID NO:233) fromArabidopsis thaliana, which encodes a 159 amino acid anaphase promotingcomplex/cyclosome subunit protein. However, it is also possible thatthis is natural variant transcript produced by the plant, becausemultiple annotations for locus At1g78770 were found in public domain.Evaluation of low-nitrogen tolerance for ME04204 in T₂ and T₃ wasconducted under the same conditions as described in Examples 2 and 3. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -01 and -05, showedsignificantly increased photosynthetic efficiency relative to theinternal controls in both generations at p≦0.05 using a one-tailedt-test assuming unequal variance. A summary of photosynthetic efficiencyof ME04204 seedlings is shown in Table 15. Events -01 and -05 segregated3:1 (R:S) for FINALE™ resistance in the T₂ generation. ME04204 eventswere also tested for enhanced growth on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 15 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Transgenic Non-Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME04204 ME04204-01 (T₂) 0.623676 340.585504 121 2.15 × 10⁻⁴ ME04204 ME04204-01 (T₃) 0.627706 17 0.585504121 8.22 × 10⁻⁵ ME04204 ME04204-05 (T₂) 0.615857 35 0.585504 121 9.41 ×10⁻³ ME04204 ME04204-05 (T₃₎ 0.611419 43 0.585504 121 1.25 × 10⁻²

Events -01 and -05 of ME04204 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 16 Analysis of ME04477 Events

ME04477 contains Ceres Clone:24255 (At2g36320, SEQ ID NO:245) fromArabidopsis thaliana, which encodes a 161 amino acid DNA binding/zincion binding protein. Evaluation of low-nitrogen tolerance for ME04477 inT₂ and T₃ was conducted under the same conditions as described inExample 2. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, -01and -05, showed significantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME04477 seedlings isshown in Table 16. Events -01 and -05 segregated 3:1 (R:S) for FINALE™resistance in the T₂ generation. ME04477 events were also tested forenhanced growth on the low nitrate media. No significant differencesbetween the transgenics and the controls were observed.

TABLE 16 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Transgenic Non-Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME04204 ME04204-01 (T₂) 0.623676 340.585504 121 2.15 × 10⁻⁴ ME04204 ME04204-01 (T₃) 0.627706 17 0.585504121 8.22 × 10⁻⁵ ME04204 ME04204-05 (T₂) 0.615857 35 0.585504 121 9.41 ×10⁻³ ME04204 ME04204-05 (T₃) 0.611419 43 0.585504 121 1.25 × 10⁻²

Events -01 and -05 of ME04477 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 17 Analysis of ME04507 Events

ME04507 contains Ceres Clone:38432 (At4g38250, SEQ ID NO:299) fromArabidopsis thaliana, which encodes a 436 amino acid transmembrane aminoacid transporter protein. Evaluation of low-nitrogen tolerance forME04507 in T₂ and T₃ was conducted under the same conditions asdescribed in Example 2. In this study, the seedling photosyntheticefficiency was measured as Fv/Fm comparing transgenic plants within anevent to non-transgenic segregants pooled across the same plate. Twoevents, -03 and -04, showed significantly increased photosyntheticefficiency on low nitrate-containing media relative to the internalcontrols in both generations at p≦0.05 using a one-tailed t-testassuming unequal variance. A summary of photosynthetic efficiency ofME04507 seedlings is shown in Table 17. Events -03 and -04 segregated15:1 and 3:1 (R:S), respectively, for FINALE™ resistance in the T₂generation. ME04507 events were also tested for enhanced growth on thelow nitrate media. No significant differences between the transgenicsand the controls were observed.

TABLE 17 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Transgenic Non-Transgenics t-testLine Events Fv/Fm n Fv/Fm n p-value ME04507 ME04507-03 0.57753 400.53084 103 4.90 × 10⁻⁴ (T₂) ME04507 ME04507-03 0.56318 39 0.53084 1032.64 × 10⁻² (T₃) ME04507 ME04507-04 0.57708 38 0.53084 103 6.12 × 10⁻³(T₂) ME04507 ME04507-04 0.57277 22 0.53084 103 2.35 × 10⁻² (T₃)

Events -03 and -04 of ME04507 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 18 Analysis of ME04587 Events

ME04587 contains Ceres Annot:553243 (At2g27010, SEQ ID NO:331) fromArabidopsis thaliana, which encodes a 516 amino acid cytochrome P450protein. Evaluation of low-nitrogen tolerance for ME04587 in T₂ and T₃was conducted under the same conditions as described in Example 2. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -01 and -02, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME04587 seedlings isshown in Table 18. In T₂ generation, events -01 and -02 segregated 1:1and 47:1 respectively (R:S) for FINALE™ resistance. These two eventssegregated 2:1 and 7:1 respectively (R:S) for FINALE® resistance in theT₃ generation.

TABLE 18 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Transgenic Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME04587 ME04587-01 0.6424 100.5437 30 2.48 × 10⁻³ (T₂) ME04587 ME04587-01 0.6165 25 0.5437 30 1.24 ×10⁻² (T₃) ME04587 ME04587-02 0.6022 47 0.5437 30 3.08 × 10⁻² (T₂)ME04587 ME04587-02 0.6310 43 0.5437 30 3.68 × 10⁻³ (T₃)

ME04587 events were also tested for enhanced growth on the low ammoniumnitrate media. In addition, these events were tested on low nitratemedia for increased seedling area and photosynthetic efficiency. Nostatistically significant differences between the transgenics and thecontrols were observed.

Events -01 and -02 of ME04587 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 19 Analysis of ME04753 Events

ME04753 contains Ceres Clone:1011900 (At2g21660, SEQ ID NO:367) fromArabidopsis thaliana, which encodes a 130 amino acid glycine-rich RNAbinding protein. Evaluation of low-nitrogen tolerance for ME04753 in T₂and T₃ was conducted under the same conditions as described in Examples2 and 3. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, -01and -02, showed significantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME04753 seedlings isshown in Table 19. Events -01 and -02 segregated 3:1 and 2:1respectively (R:S) for FINALE™ resistance in the T₂ generation. ME04753events were also tested for enhanced growth on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 19 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Transgenic Non-Transgenics t-testLine Events Fv/Fm n Fv/Fm n p-value ME04753 ME04753-01 (T₂) 0.49323 390.45917 66 3.17 × 10⁻² ME04753 ME04753-01 (T₃) 0.50942 26 0.45917 661.80 × 10⁻² ME04753 ME04753-02 (T₂) 0.49856 34 0.45917 66 2.43 × 10⁻²ME04753 ME04753-02 (T₃) 0.51274 27 0.45917 66 1.15 × 10⁻²

Events -01 and -02 of ME04753 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 20 Analysis of ME04772 Events

ME04772 contains Ceres Clone:5232 (At1g13380, SEQ ID NO:509) fromArabidopsis thaliana, which encodes a 188 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME04772 in T₂ and T₃was conducted under the same conditions as described in Example 2. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -02 and -04, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME04772 seedlings isshown in Table 20. Events -02 and -04 segregated 2:1 and 3:1respectively (R:S) for FINALE™ resistance in the T₂ generation. ME04772events were also tested for enhanced growth on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 20 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Transgenic Non-Transgenics t-testLine Events Fv/Fm n Fv/Fm n p-value ME04772 ME04772-02 (T₂) 0.53708 250.46204 53 3.36 × 10⁻⁵ ME04772 ME04772-02 (T₃) 0.53121 34 0.46204 531.27 × 10⁻⁴ ME04772 ME04772-04 (T₂) 0.52921 34 0.46204 53 3.71 × 10⁻⁴ME04772 ME04772-04 (T₃) 0.50272 36 0.46204 53 2.73 × 10⁻²

Events -02 and -04 of ME04772 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 21 Analysis of ME04772 Events

ME04909 contains Ceres Clone:29302 (At1g49010, SEQ ID NO:532) fromArabidopsis thaliana, which encodes a 314 amino acid Myb-likeDNA-binding domain protein. Evaluation of low-nitrogen tolerance forME04909 in T₂ and T₃ was conducted under the same conditions asdescribed in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -01 and -03, showed significantly increasedphotosynthetic efficiency on low nitrate-containing media relative tothe internal controls in both generations at p≦0.05 using a one-tailedt-test assuming unequal variance. A summary of photosynthetic efficiencyof ME04909 seedlings is shown in Table 21. Events -01 and -03 segregated15:1 (R:S) for FINALE™ resistance in the T₂ generation. ME04909 eventswere also tested for enhanced growth on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 21 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Transgenic Non-Transgenics t-test LineEvents Fv/Fm n Fv/Fm n p-value ME04909 ME04909-01 (T₂) 0.587774 310.550342 111 1.36 × 10⁻² ME04909 ME04909-01 (T₃) 0.607452 31 0.550342111 1.28 × 10⁻³ ME04909 ME04909-03 (T₂) 0.581537 41 0.550342 111  1.8 ×10⁻² ME04909 ME04909-03 (T₃) 0.609806 31 0.550342 111  4.3 × 10⁻⁵

Events -01 and -03 of ME04909 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 22 Analysis of ME05033 Events

ME05033 contains Ceres Clone:93971 (At4g19095, SEQ ID NO:555) fromArabidopsis thaliana, which encodes a 188 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME05033 in T₂ and T₃was conducted under the same conditions as described in Example 2. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -03 and -05, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME05033 seedlings isshown in Table 22. Events -03 and -05 segregated 15:1 and 2:1respectively (R:S) for FINALE™ resistance in the T₂ generation. ME05033events were also tested for enhanced growth on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 22 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05033 ME05033-03 (T₂)0.65717 46 0.62621 132 9.20 × 10⁻⁵ ME05033 ME05033-03 (T₃) 0.64956 390.62621 132 4.52 × 10⁻³ ME05033 ME05033-05 (T₂) 0.64448 29 0.62621 1323.46 × 10⁻² ME05033 ME05033-05 (T₃) 0.65537 30 0.62621 132 2.38 × 10⁻⁴

Events -03 and -05 of ME05033 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 23 Analysis of ME05194 Events

ME05194 contains Ceres cDNA:12669619 (At1g30710, SEQ ID NO:557) fromArabidopsis thaliana, which encodes a 531 amino acid electron carrierprotein. Evaluation of low-nitrogen tolerance for ME05194 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. Two events, -03 and -05, showed significantly enhanced growth on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling area at 14 days for transgenicplants within an event was compared to the seedling area fornon-transgenic segregants pooled across the same line. A summary ofenhanced growth under low nitrate growth conditions of ME05194 seedlingsis shown in Table 23. Events -03 and -05 segregated 1:1 (R:S) forFINALE™ resistance in the T₂ generation. ME05194 events were also testedfor increased photosynthetic efficiency on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 23 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Transgenic Non-Transgenics t-test Line Events Area nArea n p-value ME05194 ME05194-03 (T₂) 0.051216 38 0.040874 82 2.54 ×10⁻⁵ ME05194 ME05194-03 (T₃) 0.047042 45 0.040874 82 2.61 × 10⁻² ME05194ME05194-05 (T₂₎ 0.048746 26 0.040874 82 6.15 × 10⁻³ ME05194 ME05194-05(T₃) 0.048457 14 0.040874 82 3.03 × 10⁻²

Events -03 and -05 of ME05194 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 24 Analysis of ME05267 Events

ME05267 contains Ceres Clone:21608 (At5g49510, SEQ ID NO:592) fromArabidopsis thaliana, which encodes a 195 amino acid von Hippel-Lindaubinding protein. Evaluation of low-nitrogen tolerance for ME05267 in T₂and T₃ was conducted under the same conditions as described in Examples2 and 3. Two events, -01 and -04, showed significantly enhanced growthon low nitrate-containing media relative to the internal controls inboth generations at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling area at 14 days for transgenicplants within an event was compared to the seedling area fornon-transgenic segregants pooled across the same line. A summary ofenhanced growth under low nitrate growth conditions of ME05194 seedlingsis shown in Table 24. Events -01 and -04 segregated 15:1 (R:S) forFINALE™ resistance in the T₂ generation. ME05267 events were also testedfor increased photosynthetic efficiency on the low nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 24 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non- Transgenic Transgenics t-test Line Events Area nArea n p-value ME05267 ME05267-0 0.053263 46 0.0450197 122 4.4 × 10⁻⁵(T₂) ME05267 ME05267-01 0.051135 26 0.0450197 122 5.0 × 10⁻² (T₃)ME05267 ME05267-04 0.049977 44 0.0450197 122 6.4 × 10⁻³ (T₂) ME05267ME05267-04 0.053084 38 0.0450197 122 8.4 × 10⁻⁴ (T₃)

Events -01 and -04 of ME05267 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 25 Analysis of ME05300 Events

ME05300 contains Ceres Clone:2031 (At1g72020, SEQ ID NO:612) fromArabidopsis thaliana, which encodes a 97 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME05300 in T₂generation was conducted under the same conditions as described inExamples 2 and 3. A summary of photosynthetic efficiency of ME05300seedlings is shown in Table 25. Two events, -04 and -05, showedsignificantly increased photosynthetic efficiency on low nitrate- andlow ammonium nitrate-containing media relative to the internal controlsin T₂ generation at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. In addition, twoevents, -01 and -05, showed significantly enhanced growth on lownitrate- and low ammonium nitrate-containing media relative to theinternal controls in T₂ generation at p≦0.05 using a one-tailed t-testassuming unequal variance. In this study, the seedling area fortransgenic plants within an event was compared to the seedling area fornon-transgenic segregants pooled across the same line. A summary ofenhanced growth under low nitrate and low ammonium nitrate growthconditions of ME05300 seedlings is shown in Table 26.

TABLE 25A T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after14 days of growth on low nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05300 ME05300-04 (T₂)0.6867 7 0.6488 27 1.65 × 10⁻² ME05300 ME05300-05 (T₂) 0.6839 16 0.648827 2.50 × 10⁻³

TABLE 25B T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after18 days of growth on low ammonium nitrate. Pooled Non- TransgenicTransgenics t-test Line Events Fv/Fm n Fv/Fm n p-value ME05300ME05300-04 (T₂) 0.6767 6 0.6323 32 1.68 × 10⁻² ME05300 ME05300-05 (T₂)0.6934 11 0.6323 32 7.04 × 10⁻⁴

TABLE 26A T-test comparison of seedling area between transgenicseedlings and pooled non-transgenic segregants after 14 days of growthon low nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME05300 ME05300-01 (T₂) 0.0737 18 0.0588 21 3.80 ×10⁻³ ME05300 ME05300-05 (T₂) 0.0655 16 0.0570 27 1.59 × 10⁻²

TABLE 26B T-test comparison of seedling area between transgenicseedlings and pooled non-transgenic segregants after 18 days of growthon low ammonium nitrate. Pooled Non- Transgenic Transgenics t-test LineEvents Area n Area n p-value ME05300 ME05300-01 (T₂) 0.0987 17 0.0776 293.89 × 10⁻³ ME05300 ME05300-05 (T₂) 0.1082 11 0.0776 29 1.57 × 10⁻³

Example 26 Analysis of ME05341 Events

ME05341 contains Ceres Clone:94503 (At4g14420, SEQ ID NO:645) fromArabidopsis thaliana, which encodes a 158 amino acid elicitor-likeprotein. Evaluation of low-nitrogen tolerance for ME05341 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. Two events, -01 and -02, showed significantly enhanced growth on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling area at 14 days for transgenicplants within an event was compared to the seedling area fornon-transgenic segregants pooled across the same line. A summary ofphotosynthetic efficiency of ME05341 seedlings is shown in Table 27.Events -01 and -02 segregated 15:1 (R:S) for FINALE™ resistance in theT₂ generation. ME05341 events were also tested for increasedphotosynthetic efficiency on the low nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 27 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non- Transgenic Transgenics t-test Line Events Area nArea n p-value ME05341 ME05341-01 (T₂) 0.06253 46 0.04988 143 4.17 ×10⁻¹⁰ ME05341 ME05341-01 (T₃) 0.05876 38 0.04988 143 4.13 × 10⁻⁴ ME05341 ME05341-02 (T₂) 0.06152 46 0.04988 143 2.91 × 10⁻⁷  ME05341ME05341-02 (T₃) 0.05572 48 0.04988 143 2.90 × 10⁻³ 

Events -01 and -02 of ME05341 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 27 Analysis of ME05392 Events

ME05392 contains Ceres Clone:21740 (At5g01610, SEQ ID NO:686) fromArabidopsis thaliana, which encodes a 170 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME05392 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -01 and -03, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME05392 seedlings isshown in Table 20. Events -01 and -03 segregated 2:1 (R:S) for FINALE™resistance in the T₂ generation. ME05392 events were also tested forenhanced growth on the low nitrate media. No significant differencesbetween the transgenics and the controls were observed.

TABLE 28 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05392 ME05392-01 (T₂)0.61759 32 0.60093 107 3.70 × 10⁻² ME05392 ME05392-01 (T₃) 0.63388 400.60093 107 5.05 × 10⁻⁵ ME05392 ME05392-03 (T₂) 0.64335 23 0.60093 1075.81 × 10⁻⁵ ME05392 ME05392-03 (T₃) 0.63397 36 0.60093 107 4.30 × 10⁻⁵

Events -01 and -03 of ME05392 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 28 Analysis of ME05429 Events

ME05429 contains Ceres Clone:5609 (At3g60480, SEQ ID NO:729) fromArabidopsis thaliana, which encodes a 188 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME05429 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -06 and -08, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME05429 seedlings isshown in Table 29. Events -06 and -08 segregated 3:1 and 2:1respectively (R:S) for FINALE™ resistance in the T₂ generation. ME05429events were tested for enhanced growth on the low ammonium nitratemedia. In addition, these events were also tested for enhanced growthand photosynthetic efficiency on low nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 29 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05429 ME05429-06 (T₂)0.62521 28 0.59991 78 2.85 × 10⁻² ME05429 ME05429-06 (T₃) 0.63031 390.59991 78 8.49 × 10⁻³ ME05429 ME05429-08 (T₂) 0.64526 23 0.59991 781.67 × 10⁻³ ME05429 ME05429-08 (T₃) 0.65076 17 0.59991 78 2.76 × 10⁻⁴

Events -06 and -08 of ME05429 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 29 Analysis of ME05493 Events

ME05493 contains Ceres Clone:3137 (At3g43430, SEQ ID NO:745) fromArabidopsis thaliana, which encodes a 169 amino acid zinc finger familyprotein. Evaluation of low-nitrogen tolerance for ME05493 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -01 and -05, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME05493 seedlings isshown in Table 30. Events -01 and -05 segregated 15:1 (R:S) for FINALE™resistance in the T₂ generation. ME05493 events were also tested forenhanced growth on the low nitrate media. No significant differencesbetween the transgenics and the controls were observed.

TABLE 30 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05493 ME05493-01 (T₂)0.64121 32 0.61097 92 1.13 × 10⁻³ ME05493 ME05493-01 (T₃) 0.64250 460.61097 92 3.03 × 10⁻⁴ ME05493 ME05493-05 (T₂) 0.62865 43 0.61097 921.75 × 10⁻² ME05493 ME05493-05 (T₃) 0.63936 42 0.61097 92 1.21 × 10⁻⁴

Events -01 and -05 of ME05493 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 30 Analysis of ME05885 Event

ME05885 contains Ceres Clone:32430 (At1g16170, SEQ ID NO:768) fromArabidopsis thaliana, which encodes a 92 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME05885 in T₃generation was conducted under the same conditions as described inExamples 2 and 3. A summary of photosynthetic efficiency of ME05885seedlings is shown in Table 31. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -01 and -05, showed significantly increasedphotosynthetic efficiency on low nitrate-containing media and lowammonium nitrate-containing media relative to the internal controls inT₃ generation at p≦0.05 using a one-tailed t-test assuming unequalvariance.

TABLE 31A T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after14 days of growth on low nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME05885 ME05885-01 (T₃)0.6759 12 0.6533 28 4.32 × 10⁻² ME05885 ME05885-05 (T₃) 0.6831 7 0.653052 3.68 × 10⁻⁶

TABLE 31B T-test comparison of seedling photosynthetic efficiencybetween transgenic seedlings and pooled non-transgenic segregants after18 days of growth on low ammonium nitrate. Pooled Non- TransgenicTransgenics t-test Line Events Fv/Fm n Fv/Fm n p-value ME05885ME05885-01 (T₃) 0.6490 13 0.6135 30 3.06 × 10⁻² ME05885 ME05885-05 (T₃)0.6810 9 0.6133 43 6.77 × 10⁻⁵

ME05885 events were also tested for enhanced growth on the low nitrateand low ammonium nitrate media. A summary of enhanced growth under lownitrate and low ammonium nitrate growth conditions of ME05885 seedlingsin T₃ generation is shown in Table 32. Two events, -03 and -05, showedsignificantly enhanced growth on low nitrate-containing media. Twoevents, -02 and -05, showed significantly enhanced growth on lowammonium nitrate-containing media relative to the internal controls atp≦0.05 using a one-tailed t-test assuming unequal variance. In thisstudy, the seedling area for transgenic plants within an event wascompared to the seedling area for non-transgenic segregants pooledacross the same line.

TABLE 32A T-test comparison of seedling area between transgenicseedlings and pooled non-transgenic segregants after 14 days of growthon low nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME05885 ME05885-03 (T₃) 0.06245 6 0.05286 14 1.42× 10⁻² ME05885 ME05885-05 (T₃) 0.05893 7 0.04725 12 5.61 × 10⁻³

TABLE 32B T-test comparison of seedling area between transgenicseedlings and pooled non-transgenic segregants after 18 days of growthon low ammonium nitrate. Pooled Non- Transgenic Transgenics t-test LineEvents Area n Area n p-value ME05885 ME05885-02 (T₃) 0.0744 14 0.05595 63.28 × 10⁻⁵ ME05885 ME05885-05 (T₃) 0.0753 9 0.06179 11 5.08 × 10⁻³

Example 31 Analysis of ME07344 Events

ME07344 contains Ceres Clone:101255 (At2g19810, SEQ ID NO:791) fromArabidopsis thaliana, which encodes a 359 amino acid CCCH-type zincfinger protein. Evaluation of low-nitrogen tolerance for ME07344 in T₂and T₃ was conducted under the same conditions as described in Example4. In this study, the 4^(th) true leaf from each plant was collected onday 38 and analyzed on the CF imager for its Fv/Fm value. Transgenicplants within an event were compared to all non-transgenic plants,including the non-transgenic segregants and external controls. Twoevents, -02 and -03, showed significantly increased photosyntheticefficiency relative to the internal controls in both generations atp≦0.05 using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME07344 seedlings is shown in Table 33.Events -02 and -03 segregated 3:1 (R:S) for FINALE™ resistance in the T₂generation. ME07344 events were also tested for enhanced growth on thelow nitrate media. No significant differences between the transgenicsand the controls were observed.

TABLE 33 T-test comparison of photosynthetic efficiency betweentransgenic plants and non-transgenic controls after 38 days of growth onnitrogen-depleted soil. Non- Transgenic Transgenic Controls t-test LineEvents Fv/Fm n Fv/Fm n p-value ME07344 ME07344-02 (T₂) 0.752 17 0.729 502.86 × 10⁻⁴ ME07344 ME07344-02 (T₃) 0.750 16 0.729 50 1.11 × 10⁻⁴ME07344 ME07344-03 (T₂) 0.741 13 0.729 50 0.018 ME07344 ME07344-03 (T₃)0.754 17 0.729 50 4.62 × 10⁻⁶

Events -02 and -03 of ME07344 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 32 Analysis of ME07859 Events

ME07859 contains Ceres Clone:276809 (SEQ ID NO:823) from Zea mays, whichencodes a 135 amino acid sterol desaturase protein. Evaluation oflow-nitrogen tolerance for ME07859 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -02 and -04, showed significantlyincreased photosynthetic efficiency on low nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME07859 seedlings is shown in Table 34. Events -02 and -04segregated 1:1 and 2:1 respectively (R:S) for FINALE™ resistance in theT₂ generation. ME07859 events were also tested for enhanced growth onthe low nitrate media as well as for enhanced growth and photosyntheticefficiency on low ammonium nitrate media. No significant differencesbetween the transgenics and the controls were observed.

TABLE 34 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non- Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME07859 ME07859-02 (T₂)0.6598 24 0.6378 127 0.03 ME07859 ME07859-02 (T₃) 0.6825 14 0.6378 1271.3 × 10⁻³ ME07859 ME07859-04 (T₂) 0.6539 33 0.6378 127 0.05 ME07859ME07859-04 (T₃) 0.6601 17 0.6378 127 0.05

Events -02 and -04 of ME07859 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 33 Analysis of ME08464 Events

ME08464 contains Ceres Clone:424522 (SEQ ID NO:827) from Zea mays, whichencodes a 500 amino acid unknown protein. Evaluation of low-nitrogentolerance for ME08464 in T₂ and T₃ was conducted under the sameconditions as described in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -02 and -03, showed significantly increasedphotosynthetic efficiency on low ammonium nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME07859 seedlings is shown in Table 35. Events -02 and -03segregated 3:1 (R:S) for FINALE™ resistance in the T₂ generation.ME08464 events were also tested for increased photosynthetic efficiencyon the low nitrate media. No significant differences between thetransgenics and the controls were observed.

TABLE 35 T-test comparison of photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 15 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME08464 ME08464-02 (T₂) 0.6541 0.62 40 0.015 ME08464 ME08464-02 (T₃) 0.67 32 0.62 40 2.32 × 10⁻⁴ME08464 ME08464-03 (T₂) 0.65 43 0.62 40 0.013 ME08464 ME08464-03 (T₃)0.65 42 0.62 40 6.85 × 10⁻³

Events -02 and -03 of ME08464 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill)

Example 34 Analysis of ME09939 Events

ME09939 contains Ceres Clone:324216 (SEQ ID NO:852) from Zea mays, whichencodes a 38 amino acid protein of unknown function. Evaluation oflow-nitrogen tolerance for ME09939 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -04 and -05, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in both generations at p≦0.05using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME09939 seedlings is shown in Table 36.Events -04 and -05 segregated 15:1 and 3:1 respectively (R:S) forFINALE™ resistance in the T₂ generation. ME09939 events were also testedfor enhanced growth on the low ammonium nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 36 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME09939 ME09939-04 (T₂)0.49285 40 0.38571 7 0.05 ME09939 ME09939-04 (T₃) 0.50697 34 0.38571 73.50 × 10⁻² ME09939 ME09939-05 (T₂) 0.53487 39 0.47492 24 1.19 × 10⁻²ME09939 ME09939-05 (T₃) 0.55341 32 0.47492 24 1.82 × 10⁻³

Events -04 and -05 of ME09939 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 35 Analysis of ME11735 Events

ME11735 contains Ceres Annot:573161 (At5g43260, SEQ ID NO:854) fromArabidopsis thaliana, which encodes a 97 amino acid DnaJ-relatedchaperone protein. Evaluation of low-nitrogen tolerance for ME11735 inT₂ and T₃ was conducted under the same conditions as described inExample 2 and 3. A summary of the enhanced growth of ME11735 events onlow nitrate-containing media is shown in Table 37. In this study, theseedling area for transgenic plants within an event was compared to theseedling area for non-transgenic segregants pooled across the same line.Two events, -04 and -05, were found significantly larger than the poolednon-transgenic segregants after 14 days of growth on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. ME11735 events were also tested for increased photosyntheticefficiency on the low nitrate media. No significant differences betweenthe transgenics and the controls were observed. Events -04 and -05segregated 40:1 and 4:1 respectively (R:S) for FINALE™ resistance in theT₂ generation.

TABLE 37 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Transgenic Pooled Non-Transgenics t-test Line Events Area nArea n p-value ME11735 ME11735-04 (T₂) 0.05820 41 0.04994 127 5.91 ×10⁻⁵ ME11735 ME11735-04 (T₃) 0.05553 42 0.04994 127 1.26 × 10⁻² ME11735ME11735-05 (T₂) 0.05788 37 0.04994 127 1.59 × 10⁻³ ME11735 ME11735-05(T₃) 0.06011 13 0.04994 127 1.64 × 10⁻²

Events -04 and -05 of ME11735 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 36 Analysis of ME12910 Events

ME12910 contains Ceres Annot:552727 (At2g22930, SEQ ID NO:890) fromArabidopsis thaliana, which encodes a 442 amino acid UDP-glucoronosyland UDP-glucosyl transferase family protein. Evaluation of low-nitrogentolerance for ME12910 in T₂ and T₃ was conducted under the sameconditions as described in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -03 and -05, showed significantly increasedphotosynthetic efficiency on low ammonium nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME12910 seedlings is shown in Table 38. ME12910 eventswere also tested for enhanced growth on the low ammonium nitrate media.No significant differences between the transgenics and the controls wereobserved.

TABLE 38 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME12910 ME12910-03 (T₂)0.5851 39 0.5191 29 1.54 × 10⁻³ ME12910 ME12910-03 (T₃) 0.5861 22 0.519129 2.17 × 10⁻³ ME12910 ME12910-05 (T₂) 0.5523 44 0.4251 7 1.23 × 10⁻²ME12910 ME12910-05 (T₃) 0.5600 42 0.4251 7 9.62 × 10⁻³

Events -03 and -05 segregated 3:1 and 15:1 respectively (R:S) forFINALE™ resistance in the T₂ generation.

Events -03 and -05 of ME12910 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill)

Example 37 Analysis of ME12927 Event

ME12927 contains Ceres Clone:239806 (SEQ ID NO:916) from Zea mays, whichencodes a 201 amino acid lipoprotein amino terminal region. Evaluationof low-nitrogen tolerance for ME12927 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Three events, -02, -03 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05, using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME12927 seedlings isshown in Table 39.

TABLE 39 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME12927 ME12927-02 (T₂)0.60843 44 0.47813 8 4.88 × 10⁻³ ME12927 ME12927-02 (T₃) 0.60867 360.47813 8 5.23 × 10⁻³ ME12927 ME12927-03 (T₂) 0.61906 32 0.57929 38 8.96× 10⁻³ ME12927 ME12927-03 (T₃) 0.63437 19 0.57929 38 5.35 × 10⁻⁴ ME12927ME12927-05 (T₂) 0.60581 43 0.53982 22 7.26 × 10⁻³ ME12927 ME12927-05(T₃) 0.63145 29 0.53982 22 5.83 × 10⁻⁴

ME12927 events were also tested for enhanced growth on the low ammoniumnitrate media. A summary of the enhanced growth of ME11735 events on lowammonium nitrate-containing media is shown in Table 40. In this study,the seedling area for transgenic plants within an event was compared tothe seedling area for non-transgenic segregants pooled across the sameline. Three events, -02, -03 and -05, were found significantly largerthan the pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate-containing media relative to the internal controls inboth generations at p≦0.05, using a one-tailed t-test assuming unequalvariance.

TABLE 40 t-test comparison of seedling area between transgenic seedlingsand pooled non- transgenic segregants after 18 days of growth on lowammonium nitrate. Transgenic Pooled Non-Transgenics t-test Line EventsArea n Area n p-value ME12927 ME12927-02 (T₂) 0.066920 44 0.056585 1171.65 × 10⁻⁴ ME12927 ME12927-02 (T₃) 0.062119 36 0.056585 117 3.51 × 10⁻²ME12927 ME12927-03 (T₂) 0.068972 32 0.056585 117 1.18 × 10⁻⁵ ME12927ME12927-03 (T₃) 0.063716 19 0.056585 117 1.98 × 10⁻² ME12927 ME12927-05(T₂) 0.069972 43 0.056585 117 4.25 × 10⁻⁶ ME12927 ME12927-05 (T₃)0.064014 29 0.056585 117 8.49 × 10⁻³

Events 02, -03 and -05 segregated 15:1, 2:1 and 15:1 respectively (R:S)for FINALE™ resistance in the T₂ generation.

Events 02, -03 and -05 of ME12927 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill) in T₁ generation.

Example 38 Analysis of ME12929 Events

ME12929 contains Ceres Clone:208995 (SEQ ID NO:943) from Zea mays, whichencodes a 94 amino acid protein of unknown function. Evaluation oflow-nitrogen tolerance for ME12929 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -03 and -04, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in both generations at p≦0.05using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME12929 seedlings is shown in Table 41.ME12929 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed. Events -03 and -04 segregated 1:1 and 3:1respectively (R:S) for FINALE™ resistance in the T₂ generation.

TABLE 41 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME12929 ME12929-03 (T₂)0.6410 33 0.5736 24 9.44 × 10⁻⁴ ME12929 ME12929-03 (T₃) 0.6610 41 0.573624 4.38 × 10⁻⁵ ME12929 ME12929-04 (T₂) 0.6544 47 0.5790 9 3.68 × 10⁻²ME12929 ME12929-04 (T₃) 0.6663 43 0.5790 9 2.15 × 10⁻²

Events -03 and -04 of ME12929 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill)

Example 39 0020Analysis of ME12954 Events

ME12954 contains Ceres Clone:225681 (SEQ ID NO:975) from Zea mays, whichencodes a 286 amino acid protein of unknown function. Evaluation oflow-nitrogen tolerance for ME12954 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. Two events, -04 and-05, showed significantly increased photosynthetic efficiency on lowammonium nitrate-containing media relative to the internal controls inboth generations at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. A summary ofphotosynthetic efficiency of ME12954 seedlings is shown in Table 42.

TABLE 42 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME12954 ME12954-04 (T₂)0.6236 40 0.5973 152 6.61 × 10⁻³ ME12954 ME12954-04 (T₃) 0.6200 390.5973 152 1.97 × 10⁻² ME12954 ME12954-05 (T₂) 0.6280 45 0.5973 152 1.79× 10⁻² ME12954 ME12954-05 (T₃) 0.6315 35 0.5973 152 2.85 × 10⁻²

ME12954 events were also tested for enhanced growth on the low ammoniumnitrate media. A summary of the enhanced growth of ME12954 events on lowammonium nitrate-containing media is shown in Table 43. In this study,the seedling area for transgenic plants within an event was compared tothe seedling area for non-transgenic segregants pooled across the sameline. Two events, -02 and -04, were found significantly larger than thepooled non-transgenic segregants after 18 days of growth on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05, using a one-tailed t-test assuming unequalvariance.

TABLE 43 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Transgenic Pooled Non-Transgenics t-test Line EventsArea n Area n p-value ME12954 ME12954-02 (T₂) 0.06883 31 0.05579 1521.86 × 10⁻⁵ ME12954 ME12954-02 (T₃) 0.06604 26 0.05579 152 1.48 × 10⁻³ME12954 ME12954-04 (T₂) 0.06469 40 0.05579 152 1.95 × 10⁻⁴ ME12954ME12954-04 (T₃) 0.06301 39 0.05579 152 3.32 × 10⁻³

Events -02, -04 and -05 segregated 2:1, 3:1 and 15:1 respectively (R:S)for FINALE™ resistance in the T2 generation.

Events -02, -04 and -05 of ME12954 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 40 Analysis of ME12970 Events

ME12970 contains Ceres Clone:1387146 (SEQ ID NO:981) from Zea mays,which encodes a 147 amino acid C2 domain-containing protein. Evaluationof low-nitrogen tolerance for ME12970 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. Two events, -02and -03, showed significantly increased photosynthetic efficiency on lowammonium nitrate-containing media relative to the internal controls inboth generations at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. A summary ofphotosynthetic efficiency of ME12970 seedlings is shown in Table 44.ME12970 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 44 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME12970 ME12970-02 (T₂)0.55136 44 0.52401 108 3.78 × 10⁻² ME12970 ME12970-02 (T₃) 0.58305 430.52401 108 1.89 × 10⁻⁵ ME12970 ME12970-03 (T₂) 0.58759 37 0.52401 1082.14 × 10⁻⁶ ME12970 ME12970-03 (T₃) 0.59131 29 0.52401 108 3.05 × 10⁻⁶

Events -02 and -03 segregated 15:1 and 3:1 respectively (R:S) forFINALE™ resistance in the T2 generation.

Events -02 and -03 of ME12970 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 41 Analysis of ME13006 Events

ME13006 contains Ceres Clone:1017441 (SEQ ID NO:224) from Triticumaestivum, which encodes a 143 amino acid polypeptide, predicted to be ahomolog of Ceres Clone:4898 (ME03123, SEQ ID NO:217). Evaluation oflow-nitrogen tolerance for ME13006 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -01 and -03, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in both generations at p≦0.05using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME13006 seedlings is shown in Table 45.ME13006 events were also tested for enhanced growth on the low nitratemedia. No significant differences between the transgenics and thecontrols were observed.

TABLE 45 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lowammonium nitrate. Transgenic Pooled Non-Transgenics t-test Line EventsArea n Area n p-value ME13006 ME13006-01 (T₂) 0.0777 42 0.0648 7 3.29 ×10⁻² ME13006 ME13006-01 (T₃) 0.0660 28 0.0540 19 1.49 × 10⁻³ ME13006ME13006-03 (T₂) 0.0706 21 0.0601 29 4.83 × 10⁻³ ME13006 ME13006-03 (T₃)0.0758 14 0.0617 33 2.60 × 10⁻³

Events -01 and -03 segregated 3:1 and 1:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -01 and -03 of ME13006 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 42 Analysis of ME13021 Events

ME13021 contains Ceres Clone:244306 (SEQ ID NO:1053) from Zea mays,which encodes a 572 amino acid TCP-1/cpn60 chaperonin family protein.Evaluation of low-nitrogen tolerance for ME13021 in T₂ and T₃ wasconducted under the same conditions as described in Examples 2 and 3. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -04 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13021 seedlings isshown in Table 46. ME13021 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 46 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13021 ME13021-04 (T₂)0.56697 39 0.49440 10 2.47 × 10⁻² ME13021 ME13021-04 (T₃) 0.59916 370.48685 13 1.54 × 10⁻³ ME13021 ME13021-05 (T₂) 0.60575 32 0.50344 186.05 × 10⁻⁴ ME13021 ME13021-05 (T₃) 0.64400 23 0.55638 26 3.86 × 10⁻⁶

Events -04 and -05 segregated 3:1 and 2:1 respectively (R:S) for FINALE™resistance in the T2 generation.

Events -04 and -05 of ME13021 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill) in T1 generation.

Example 43 Analysis of ME13064 Events

ME13064 contains Ceres Clone:1408950 (SEQ ID NO:1098) from Zea mays,which encodes a 152 amino acid protein of unknown function. Evaluationof low-nitrogen tolerance for ME13064 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -03 and -04, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in both generations at p≦0.05using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME13064 seedlings is shown in Table 47.ME13064 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 47 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13064 ME13064-03 (T₂)0.59444 27 0.54793 28 5.84 × 10⁻³ ME13064 ME13064-03 (T₃) 0.59676 290.54793 28 1.25 × 10⁻² ME13064 ME13064-04 (T₂) 0.58577 31 0.51053 402.05 × 10⁻³ ME13064 ME13064-04 (T₃) 0.59128 25 0.51053 40 8.93 × 10⁻⁴

Events -03 and -04 segregated 2:1 (R:S) for FINALE™ resistance in the T2generation.

Events -03 and -04 of ME13064 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill) in T1 generation.

Example 44 Analysis of ME13071 Events

ME13071 contains Ceres Clone:208453 (SEQ ID NO:1111) from Zea mays,which encodes a 74 amino acid protein of unknown function. Evaluation oflow-nitrogen tolerance for ME13071 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. Two events, -03 and-05, showed significantly enhanced growth on low nitrate- and lowammonium nitrate-containing media relative to the internal controls inT₂ generation at p≦0.05 using a one-tailed t-test assuming unequalvariance. In this study, the seedling area for transgenic plants withinan event was compared to the seedling area for non-transgenic segregantspooled across the same line. A summary of enhanced growth under lowammonium nitrate growth conditions of ME13071 seedlings is shown inTable 48. ME13071 events were also tested for photosynthetic efficiencyon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 48 t-test comparison of seedling area between transgenic seedlingsand pooled non- transgenic segregants after 18 days of growth on lowammonium nitrate. Transgenic Pooled Non-Transgenics t-test Line EventsArea n Area n p-value ME13071 ME13071-03 (T₂) 0.06694 26 0.05915 19 3.55× 10⁻³ ME13071 ME13071-03 (T₃) 0.07787 24 0.07040 22 3.65 × 10⁻² ME13071ME13071-05 (T₂) 0.06232 32 0.05491 16 2.07 × 10⁻³ ME13071 ME13071-05(T₃) 0.06335 22 0.05626 28 1.09 × 10⁻²

Events -03 and -05 segregated 1:1 and 2:1 respectively (R:S) for FINALE™resistance in the T2 generation.

Events -03 and -05 of ME13071 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 45 Analysis of ME13087 Events

ME13087 contains Ceres Clone:968180 (SEQ ID NO:1115) from Brassicanapus, which encodes a 159 amino acid zinc finger protein. Evaluation oflow-nitrogen tolerance for ME13087 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Four events, -01, -02, -03 and -04, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13087 seedlings isshown in Table 49. ME13087 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 49 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Transgenic Pooled Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13087 ME13087-01 (T₂)0.59761 23 0.56163 38 9.61 × 10⁻³ ME13087 ME13087-01 (T₃) 0.61247 150.56163 38 5.99 × 10⁻⁴ ME13087 ME13087-02 (T₂) 0.63400 39 0.58532 349.30 × 10⁻³ ME13087 ME13087-02 (T₃) 0.63442 26 0.58532 34 1.22 × 10⁻²ME13087 ME13087-03 (T₂) 0.61429 38 0.55533 24 5.04 × 10⁻³ ME13087ME13087-03 (T₃) 0.62283 35 0.55533 24 3.31 × 10⁻³ ME13087 ME13087-04(T₂) 0.62714 28 0.60068 56 3.02 × 10⁻² ME13087 ME13087-04 (T₃) 0.64543 70.60068 56 9.04 × 10⁻³

Events -01, -02, -03 and -04 segregated 2:1, 3:1, 3:1 and 2:1respectively (R:S) for FINALE™ resistance in the T2 generation.

Events -01, -02, -03 and -04 of ME13087 exhibited no statisticallyrelevant negative phenotypes. That is, there was no detectable reductionin germination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill) in T1 generation

Example 46 Analysis of ME13106 Events

ME13106 contains Ceres Clone:986438 (SEQ ID NO:1156) from Zea mays,which encodes a 188 amino acid protein of unknown function. Evaluationof low-nitrogen tolerance for ME13106 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -03 and -04, showed significantlyincreased photosynthetic efficiency on low ammonium nitrate-containingmedia relative to the internal controls in both generations at p≦0.05using a one-tailed t-test assuming unequal variance. A summary ofphotosynthetic efficiency of ME13106 seedlings is shown in Table 50.ME13106 events were also tested for enhanced growth on the low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 50 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13106 ME13106-03 (T₂)0.62726 27 0.58600 43 1.50 × 10⁻² ME13106 ME13106-03 (T₃) 0.65163 300.58600 43 1.69 × 10⁻⁴ ME13106 ME13106-04 (T₂) 0.60836 36 0.55876 252.62 × 10⁻² ME13106 ME13106-04 (T₃) 0.64250 38 0.55876 25 5.01 × 10⁻⁴

Events -03 and -04 segregated 1:1 and 3:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -03 and -04 of ME13106 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill)

Example 47 Analysis of ME13107 Events

ME13107 contains Ceres Clone:996227 (SEQ ID NO:1158) from Zea mays,which encodes a 240 amino acid zein seed storage protein. Evaluation oflow-nitrogen tolerance for ME13107 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Three events, -02, -04 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13107 seedlings isshown in Table 51.

TABLE 51 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13107 ME13107-02 (T₂)0.63122 37 0.56643 21 1.07 × 10⁻² ME13107 ME13107-02 (T₃) 0.63848 290.56643 21 6.03 × 10⁻³ ME13107 ME13107-04 (T₂) 0.62948 27 0.55918 502.07 × 10⁻⁵ ME13107 ME13107-04 (T₃) 0.63019 21 0.55918 50 6.72 × 10⁻⁵ME13107 ME13107-05 (T₂) 0.61952 29 0.54440 48 7.85 × 10⁻⁵ ME13107ME13107-05 (T₃) 0.62185 20 0.54440 48 4.02 × 10⁻⁵

ME13107 events were also tested for enhanced growth on the low ammoniumnitrate media. Two events, -02 and -04, showed significantly enhancedgrowth on low ammonium nitrate-containing media relative to the internalcontrols in T₂ generation at p≦0.05 using a one-tailed t-test assumingunequal variance. In this study, the seedling area for transgenic plantswithin an event was compared to the seedling area for non-transgenicsegregants pooled across the same line. A summary of enhanced growthunder low ammonium nitrate growth conditions of ME13071 seedlings isshown in Table 52.

TABLE 52 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non- Transgenic Transgenics t-test Line EventsArea n Area n p-value ME13107 ME13107-02 (T₂) 0.07738 37 0.06919 2033.63 × 10⁻² ME13107 ME13107-02 (T₃) 0.07688 29 0.06919 203 4.60 × 10⁻²ME13107 ME13107-04 (T₂) 0.07514 27 0.06919 203 3.18 × 10⁻² ME13107ME13107-04 (T₃) 0.07585 21 0.06919 203 2.27 × 10⁻²

Events -02, -04 and -05 segregated 3:1, 1:1 and 2:1 respectively (R:S)for FINALE™ resistance in the T₂ generation.

Events -02, -04 and -05 of ME13107 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 48 Analysis of ME13108 Events

ME13108 contains Ceres Clone:996263 (SEQ ID NO:1165) from Zea mays,which encodes an 84 amino acid BRICK1 protein. Evaluation oflow-nitrogen tolerance for ME13108 in T₂ and T₃ was conducted under thesame conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Three events, -01, -04 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13108 seedlings isshown in Table 53. ME13108 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 53 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13108 ME13108-01 (T₂)0.56703 36 0.53932 195 1.97 × 10⁻² ME13108 ME13108-01 (T₃) 0.59250 260.53932 195 3.64 × 10⁻⁴ ME13108 ME13108-04 (T₂) 0.60032 37 0.53932 1953.37 × 10⁻⁷ ME13108 ME13108-04 (T₃) 0.60463 30 0.53932 195 4.10 × 10⁻⁵ME13108 ME13108-05 (T₂) 0.60727 30 0.53932 195 4.97 × 10⁻⁹ ME13108ME13108-05 (T₃) 0.61850 32 0.53932 195 2.35 × 10⁻⁹

Events -01, -04 and -05 segregated 3:1 (R:S) for FINALE™ resistance inthe T₂ generation.

Events -01, -04 and -05 of ME13108 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 49 Analysis of ME13110 Events

ME13110 contains Ceres Clone:988083 (SEQ ID NO:1184) from Zea mays,which encodes a 188 amino acid protein of unknown function. Evaluationof low-nitrogen tolerance for ME13110 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Three events, -03, -04 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13110 seedlings isshown in Table 54. ME13110 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 54 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13110 ME13110-03 (T₂)0.5721 34 0.3948 16 8.92 × 10⁻³ ME13110 ME13110-03 (T₃) 0.5773 24 0.458326 4.58 × 10⁻⁴ ME13110 ME13110-04 (T₂) 0.5651 35 0.4243 15 4.34 × 10⁻²ME13110 ME13110-04 (T₃) 0.6000 10 0.4594 40 3.29 × 10⁻³ ME13110ME13110-05 (T₂) 0.5143 28 0.3809 22 2.24 × 10⁻² ME13110 ME13110-05 (T₃)0.5278 28 0.3688 21 1.28 × 10⁻²

Events -03, -04 and -05 segregated 3:1, 1:1 and 3:1 respectively (R:S)for FINALE™ resistance in the T₂ generation.

Events -03, -04 and -05 of ME13110 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 50 Analysis of ME13125 Events

ME13125 contains Ceres Clone:732 (At3g50880, SEQ ID NO:1193) fromArabidopsis thaliana, which encodes a 188 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME13125 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Three events, -01, -03 and -05,showed significantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13125 seedlings isshown in Table 55. ME13125 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 55 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13125 ME13125-01 (T₂)0.61129 42 0.53829 125 4.82 × 10⁻⁷ ME13125 ME13125-01 (T₃) 0.61929 380.53829 125 1.96 × 10⁻⁷ ME13125 ME13125-03 (T₂) 0.63360 45 0.53829 125 3.05 × 10⁻¹³ ME13125 ME13125-03 (T₃) 0.62218 44 0.53829 125 3.81 × 10⁻⁹ME13125 ME13125-05 (T₂) 0.61565 31 0.53829 125 4.12 × 10⁻⁸ ME13125ME13125-05 (T₃) 0.58469 16 0.53829 125 0.05

Events -01, -03 and -05 segregated 3:1, 15:1 and 2:1 respectively (R:S)for FINALE™ resistance in the T₂ generation.

Events -01, -03 and -05 of ME13125 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 51 Analysis of ME13149 Events

ME13149 contains Ceres Clone:2267 (At2g24765, SEQ ID NO:1209) fromArabidopsis thaliana, which encodes a 182 amino acid ADP-ribosylationfactor 3 protein. Evaluation of low-nitrogen tolerance for ME13149 in T₂and T₃ was conducted under the same conditions as described in Examples2 and 3. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, -02and -03, showed significantly increased photosynthetic efficiency on lowammonium nitrate-containing media relative to the internal controls inboth generations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13149 seedlings isshown in Table 56. ME13149 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 56 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13149 ME13149-02 (T₂)0.55623 30 0.51138 55 2.29 × 10⁻² ME13149 ME13149-02 (T₃) 0.54818 170.51138 55 4.56 × 10⁻² ME13149 ME13149-03 (T₂) 0.55998 42 0.51138 555.11 × 10⁻³ ME13149 ME13149-03 (T₃) 0.58450 24 0.51138 55 2.77 × 10⁻⁴

Events -02 and -03 segregated 2:1 and 15:1 respectively (R:S) forFINALE™ resistance in the T₂ generation.

Events -02 and -03 of ME13149 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 52 Analysis of ME13151 Events

ME13151 contains Ceres Clone:39358 (At3g25150, SEQ ID NO:1273) fromArabidopsis thaliana, which encodes a 488 amino acid nuclear transportfactor 2 (NTF2) domain protein. Evaluation of low-nitrogen tolerance forME13151 in T₂ and T₃ was conducted under the same conditions asdescribed in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -01 and -02, showed significantly increasedphotosynthetic efficiency on low ammonium nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME13151 seedlings is shown in Table 57. ME13151 eventswere also tested for enhanced growth on the low ammonium nitrate media.No significant differences between the transgenics and the controls wereobserved.

TABLE 57 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non- Transgenic Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13151 ME13151-01 (T₂)0.62593 44 0.53141 17 8.58 × 10⁻⁴ ME13151 ME13151-01 (T₃) 0.59936 330.53141 17 1.21 × 10⁻² ME13151 ME13151-02 (T₂) 0.59879 39 0.46956 163.08 × 10⁻⁵ ME13151 ME13151-02 (T₃) 0.59566 32 0.46956 16 4.28 × 10⁻⁵

Events -01 and -02 segregated 9:1 and 6:1 respectively (R:S) for FINALE™resistance in the T2 generation.

Events -01 and -02 of ME13151 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 53 Analysis of ME13153 Events

ME13153 contains Ceres Clone:115046 (At3g17760, SEQ ID NO:1301) fromArabidopsis thaliana, which encodes a 494 amino acid glutamatedecarboxylase. Evaluation of low-nitrogen tolerance for ME13153 in T₂and T₃ was conducted under the same conditions as described in Examples2 and 3. In this study, the seedling photosynthetic efficiency wasmeasured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Two events, -03and -04, showed significantly increased photosynthetic efficiency on lowammonium nitrate-containing media relative to the internal controls inboth generations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13153 seedlings isshown in Table 58. ME13153 events were also tested for increasedphotosynthetic efficiency on the low nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 58 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and non-transgenic segregants after 14 days ofgrowth on low ammonium nitrate. Pooled Transgenic Non-Transgenics t-testLine Events Fv/Fm n Fv/Fm n p-value ME13153 ME13153-03 (T₂) 0.62 34 0.5616 3.0 × 10⁻² ME13153 ME13153-03 (T₃) 0.60 19 0.54 22 2.9 × 10⁻² ME13153ME13153-04 (T₂) 0.57 32 0.50 18 4.3 × 10⁻² ME13153 ME13153-04 (T₃) 0.6124 0.55 24 2.1 × 10⁻²

Events -03 and -04 segregated 3:1 (R:S) for FINALE™ resistance in the T₂generation.

Events -03 and -04 of ME13153 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting. Events -03 and -04 yieldedslightly less seed per plant compared to the controls, but thesedifferences are not significant at p≦0.10.

Example 54 Analysis of ME13177 Events

ME13177 contains Ceres Clone:339439 (SEQ ID NO:1341) from Zea mays,which encodes a 345 amino acid cyclin C-terminal domain protein.Evaluation of low-nitrogen tolerance for ME13177 in T₂ and T₃ wasconducted under the same conditions as described in Examples 2 and 3. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Two events, -01 and -02, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME13177 seedlings isshown in Table 59. ME13177 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 59 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Transgenic Non-Transgenicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13177 ME13177- 0.6315 320.6112 175 2.43 × 01 (T₂) 10⁻² ME13177 ME13177- 0.6407 29 0.6112 1757.33 × 01 (T₃) 10⁻³ ME13177 ME13177- 0.6400 41 0.6112 175 1.23 × 02 (T₂)10⁻³ ME13177 ME13177- 0.6499 20 0.6112 175 6.47 × 02 (T₃) 10⁻³

Events -01 and -02 segregated 2:1 and 3:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -01 and -02 of ME13177 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 55 Analysis of ME13200 Events

ME13200 contains Ceres Clone:896483 (SEQ ID NO:1384) from Zea mays,which encodes an 85 amino acid myb family transcription factor.Evaluation of low-nitrogen tolerance for ME13200 in T₂ and T₃ wasconducted under the same conditions as described in Examples 2 and 3. Asummary of the enhanced growth of ME13200 events on low ammoniumnitrate-containing media is shown in Table 60. In this study, theseedling area for transgenic plants within an event was compared to theseedling area for non-transgenic segregants pooled across the same line.Two events, -03 and -04, were found significantly larger than the poolednon-transgenic segregants after 18 days of growth on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. ME13200 events were also tested for increased photosyntheticefficiency on the low ammonium nitrate media as well as for enhancedphotosynthesis and growth on low nitrate media. No significantdifferences between the transgenics and the controls were observed.

TABLE 60 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non-Trans- Transgenic genics t-test Line EventsArea n Area n p-value ME13200 ME13200-03 (T₂) 0.07366 43 0.06342 35 4.09× 10⁻⁴ ME13200 ME13200-03 (T₃) 0.08193 34 0.06342 35 2.37 × 10⁻⁵ ME13200ME13200-04 (T₂) 0.07377 48 0.06342 35 4.87 × 10⁻⁴ ME13200 ME13200-04(T₃) 0.07530 47 0.06342 35 1.88 × 10⁻⁴

Events -03 and -04 segregated 3:1 and 15:1 respectively (R:S) forFINALE™ resistance in the T₂ generation.

Events -03 and -04 of ME13200 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 56 Analysis of ME13204 Events

ME13204 contains Ceres Clone:995409 (SEQ ID NO:1408) from Zea mays,which encodes a 178 amino acid protein of unknown function. Evaluationof low-nitrogen tolerance for ME13204 in T₂ and T₃ was conducted underthe same conditions as described in Examples 2 and 3. In this study, theseedling photosynthetic efficiency was measured as Fv/Fm comparingtransgenic plants within an event to non-transgenic segregants pooledacross the same plate. Two events, -01 and -05, showed significantlyincreased photosynthetic efficiency on low nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME13204 seedlings is shown in Table 61. ME13204 eventswere also tested for enhanced growth on the low nitrate media as well asfor enhanced growth and photosynthetic efficiency on low ammoniumnitrate media. No significant differences between the transgenics andthe controls were observed.

TABLE 61 T-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME13204 ME13204-01 (T₂)0.5874 45 0.5354 46 1.41 × 10⁻² ME13204 ME13204-01 (T₃) 0.5932 36 0.535446 9.85 × 10⁻³ ME13204 ME13204-05 (T₂) 0.5855 34 0.5354 46 2.00 × 10⁻²ME13204 ME13204-05 (T₃) 0.5998 20 0.5354 46 5.58 × 10⁻³

Events -01 and -05 segregated 9:1 and 3:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -01 and -05 of ME13204 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 57 Analysis of ME14649 Events

ME14649 contains Ceres Annot:850581 (At5g01880, SEQ ID NO:1427) fromArabidopsis thaliana, which encodes a 159 amino acid zinc fingerprotein. Evaluation of low-nitrogen tolerance for ME14649 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -02 and -03, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME14649 seedlings isshown in Table 62. ME14649 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 62 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME14649 ME14649-02 (T₂)0.59789 35 0.54533 30 1.54 × 10⁻⁴ ME14649 ME14649-02 (T₃) 0.58154 260.54533 30 3.42 × 10⁻² ME14649 ME14649-03 (T₂) 0.61875 28 0.56539 332.03 × 10⁻³ ME14649 ME14649-03 (T₃) 0.62630 27 0.56539 33 9.18 × 10⁻⁴

Events -02 and -03 segregated 3:1 and 2:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -02 and -03 of ME14649 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill) in T1 generation.

Example 58 Analysis of ME16546 Events

ME16546 contains Ceres Annot:862321 (At2g45360, SEQ ID NO:1462) fromArabidopsis thaliana, which encodes a 215 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME16546 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -04 and -05, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME16546 seedlings isshown in Table 63. ME16546 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 63 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME16546 ME16546-04 (T₂)0.59891 33 0.56124 130 2.21 × 10⁻⁴ ME16546 ME16546-04 (T₃) 0.57924 410.56124 130 3.77 × 10⁻² ME16546 ME16546-05 (T₂) 0.58861 36 0.56124 1307.17 × 10⁻³ ME16546 ME16546-05 (T₃) 0.61763 27 0.56124 130 3.25 × 10⁻⁶

Events -04 and -05 segregated 2:1 and 3:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -04 and -05 of ME16546 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 59 Analysis of ME17457 Events

ME17457 contains Ceres Annot:839064 (At1g80600, SEQ ID NO:1478) fromArabidopsis thaliana, which encodes a 457 acetylornithineaminotransferase, a member of the Class-III aminotransferase family.This is a homolog of Ceres Clone:19586 (ME01463, SEQ ID NO:76).Evaluation of low-nitrogen tolerance for ME17457 in T₂ and T₃ wasconducted under the same conditions as described in Examples 2 and 3. Inthis study, the seedling photosynthetic efficiency was measured as Fv/Fmcomparing transgenic plants within an event to non-transgenic segregantspooled across the same plate. Four events, -02, -03, -05 and -06, showedsignificantly increased photosynthetic efficiency on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME17457 seedlings isshown in Table 64. ME17457 events were also tested for enhanced growthon the low ammonium nitrate media. No significant differences betweenthe transgenics and the controls were observed.

TABLE 64 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME17457 ME17457-02 (T₂)0.60800 21 0.50878 46 6.99 × 10⁻⁴ ME17457 ME17457-02 (T₃) 0.59539 180.50878 46 9.02 × 10⁻³ ME17457 ME17457-03 (T₂) 0.55164 11 0.49673 453.45 × 10⁻² ME17457 ME17457-03 (T₃) 0.57356 18 0.49673 45 2.49 × 10⁻³ME17457 ME17457-05 (T₂) 0.52928 18 0.42672 32 2.23 × 10⁻³ ME17457ME17457-05 (T₃) 0.56660 25 0.42672 32 5.97 × 10⁻⁵ ME17457 ME17457-06(T₂) 0.54088 33 0.47350 30 3.59 × 10⁻⁴ ME17457 ME17457-06 (T₃) 0.5221021 0.47350 30 2.03 × 10⁻²

Events -02, -03 and -05 segregated 1:1, and Event -06 segregated 3:1(R:S) for FINALE™ resistance in the T₂ generation.

Events -02, -03, -05 and -06 of ME17457 exhibited no statisticallyrelevant negative phenotypes. That is, there was no detectable reductionin germination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 60 Analysis of ME17567 Events

ME17567 contains Ceres Annot:864666 (At1g16320, SEQ ID NO:1490) fromArabidopsis thaliana, which encodes a 273 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME17567 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -01 and -04, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME17567 seedlings isshown in Table 65. ME17567 events were also tested for enhanced growthon the low nitrate media as well as enhanced photosynthetic efficiencyand growth on low ammonium nitrate media. No significant differencesbetween the transgenics and the controls were observed.

TABLE 65 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate. Pooled Non-Trans- Transgenic genics t-testLine Events Fv/Fm n Fv/Fm n p-value ME17567 ME17567- 0.605455 330.474791 67 9.69 × 01 (T₂) 10⁻¹⁰ ME17567 ME17567- 0.6244  20 0.474791 676.79 × 01 (T₃) 10⁻¹³ ME17567 ME17567- 0.57727  37 0.474791 67 1.22 × 04(T₂) 10⁻⁷ ME17567 ME17567- 0.615143 35 0.474791 67 5.95 × 04 (T₃) 10⁻¹³

Events -01 and -04 segregated 2:1 and 3:1 respectively (R:S) for FINALE™resistance in the T₂ generation.

Events -01 and -04 of ME17567 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 61 Analysis of ME17932 Events

ME17932 contains Ceres Annot:875012 (At3g53560, SEQ ID NO:1509) fromArabidopsis thaliana, which encodes a 340 amino acid chloroplast lumencommon family protein. Evaluation of low-nitrogen tolerance for ME17932in T₂ and T₃ was conducted under the same conditions as described inExamples 2 and 3. In this study, the seedling photosynthetic efficiencywas measured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Four events,-01, -02, -03 and -05, showed significantly increased photosyntheticefficiency on low ammonium nitrate-containing media relative to theinternal controls in both generations at p≦0.05 using a one-tailedt-test assuming unequal variance. A summary of photosynthetic efficiencyof ME17932 seedlings is shown in Table 66. ME17932 events were alsotested for enhanced growth on the low ammonium nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 66 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME17932 ME17932-01 (T₂)0.6292 36 0.6094 194 0.050 ME17932 ME17932-01 (T₃) 0.6640 22 0.6094 1942.82 × 10⁻⁶ ME17932 ME17932-02 (T₂) 0.6351 32 0.6094 194 1.05 × 10⁻²ME17932 ME17932-02 (T₃) 0.6373 20 0.6094 194 2.82 × 10⁻² ME17932ME17932-03 (T₂) 0.6504 45 0.6094 194 1.80 × 10⁻⁵ ME17932 ME17932-03 (T₃)0.6708 20 0.6094 194 8.38 × 10⁻⁴ ME17932 ME17932-05 (T₂) 0.6349 240.6094 194 3.23 × 10⁻² ME17932 ME17932-05 (T₃) 0.6615 11 0.6094 194 1.16× 10⁻³

Events -01, -02, -03 and -05 segregated 3:1, 2:1, 15:1 and 1:1respectively (R:S) for FINALE™ resistance in the T₂ generation.

Events -01, -02, -03 and -05 of ME17932 exhibited no statisticallyrelevant negative phenotypes. That is, there was no detectable reductionin germination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 62 Analysis of ME17936 Events

ME17936 contains Ceres Annot:874016 (At3g42800, SEQ ID NO:1524) fromArabidopsis thaliana, which encodes a 341 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME17936 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -01 and -05, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME17936 seedlings isshown in Table 67. ME17936 events were also tested for enhanced growthon the low nitrate media as well as for increased photosyntheticefficiency and enhanced growth on low ammonium nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 67 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME17936 ME17936-01 (T₂)0.64778 36 0.61762 39 4.68 × 10⁻³ ME17936 ME17936-01 (T₃) 0.66081 210.61762 39 4.33 × 10⁻⁵ ME17936 ME17936-05 (T₂) 0.63189 35 0.61444 502.73 × 10⁻² ME17936 ME17936-05 (T₃) 0.64257 14 0.61444 50 2.56 × 10⁻²

Events -01 and -05 segregated 3:1 (R:S) for FINALE™ resistance in the T₂generation.

Events -01 and -05 of ME17936 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 63 Analysis of ME18275 Events

ME18275 contains Ceres Annot:827304 (At2g18300, SEQ ID NO:1536) fromArabidopsis thaliana, which encodes a 335 amino acid helix-loop-helixDNA-binding domain. Evaluation of low-nitrogen tolerance for ME18275 inT₂ and T₃ was conducted under the same conditions as described inExamples 2 and 3. A summary of the enhanced growth of ME18275 events onlow nitrate-containing media is shown in Table 68. In this study, theseedling area for transgenic plants within an event was compared to theseedling area for non-transgenic segregants pooled across the same line.Three events, -01, -02 and -03, were found significantly larger than thepooled non-transgenic segregants after 14 days of growth on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05, using a one-tailed t-test assuming unequalvariance. ME18275 events were also tested for photosynthetic efficiencyon the low nitrate media as well as for increased photosyntheticefficiency and enhanced growth on low ammonium nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 68 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 14 days of growth on lownitrate. Pooled Non-Trans- Transgenic genics t-test Line Events Area nArea n p-value ME18275 ME18275-01 (T₂) 0.09574 40 0.05961 10  3.24 ×10⁻¹⁰ ME18275 ME18275-01 (T₃) 0.07807 32 0.05142 15 3.71 × 10⁻⁴ ME18275ME18275-02 (T₂) 0.11903 33 0.05884 16  6.21 × 10⁻¹⁴ ME18275 ME18275-02(T₃) 0.08552 22 0.04208 24 2.82 × 10⁻⁵ ME18275 ME18275-03 (T₂) 0.1028139 0.06789  9 9.48 × 10⁻⁸ ME18275 ME18275-03 (T₃) 0.09136 20 0.05646 269.46 × 10⁻⁴

Events -01, -02 and -03 segregated 3:1 (R:S) for FINALE™ resistance inthe T₂ generation.

Events -01, -02 and -03 of ME18275 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 64 Analysis of ME18924 Events

ME18924 contains Ceres Annot:869192 (At1g72160, SEQ ID NO:1553) fromArabidopsis thaliana, which encodes a 490 amino acid emp24/gp25L/p24family protein. Evaluation of low-nitrogen tolerance for ME18924 in T₂and T₃ was conducted under the same conditions as described in Examples2 and 3. A summary of photosynthetic efficiency of ME18924 seedlings isshown in Table 69. In this study, the seedling photosynthetic efficiencywas measured as Fv/Fm comparing transgenic plants within an event tonon-transgenic segregants pooled across the same plate. Three events,-02, -04 and -05, showed significantly increased photosyntheticefficiency on low ammonium nitrate-containing media relative to theinternal controls in both generations at p≦0.05, using a one-tailedt-test assuming unequal variance.

TABLE 69 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME18924 ME18924-02 (T₂)0.6515 46 0.6223 138 6.43 × 10⁻³ ME18924 ME18924-02 (T₃) 0.6639 450.6223 138 1.52 × 10⁻⁴ ME18924 ME18924-04 (T₂) 0.6489 33 0.6223 138 2.72× 10⁻³ ME18924 ME18924-04 (T₃) 0.6517 21 0.6223 138 1.58 × 10⁻² ME18924ME18924-05 (T₂) 0.6602 35 0.6223 138 5.55 × 10⁻⁵ ME18924 ME18924-05 (T₃)0.6488 31 0.6223 138 4.25 × 10⁻²

ME18924 events were also tested for enhanced growth on the low ammoniumnitrate media. A summary of the enhanced growth of ME18924 events on lownitrate-containing media is shown in Table 70. In this study, theseedling area for transgenic plants within an event was compared to theseedling area for non-transgenic segregants pooled across the same line.Two events, -01 and -04, were found significantly larger than the poolednon-transgenic segregants after 18 days of growth on low ammoniumnitrate-containing media relative to the internal controls in bothgenerations at p≦0.05, using a one-tailed t-test assuming unequalvariance.

TABLE 70 t-test comparison of seedling area between transgenic seedlingsand pooled non-transgenic segregants after 18 days of growth on lowammonium nitrate. Pooled Non-Trans- Transgenic genics t-test Line EventsArea n Area n p-value ME18924 ME18924-01 (T₂) 0.06881 37 0.06311 1381.31 × 10⁻² ME18924 ME18924-01 (T₃) 0.07164 34 0.06311 138 7.43 × 10⁻³ME18924 ME18924-04 (T₂) 0.08401 33 0.06311 138 5.64 × 10⁻⁸ ME18924ME18924-04 (T₃) 0.07365 21 0.06311 138 3.82 × 10⁻²

Events -01, -02, -04 and -05 segregated 3:1, 15:1, 2:1 and 2:1respectively (R:S) for FINALE™ resistance in the T₂ generation.

Events -01, -02, -04 and -05 of ME18924 exhibited no statisticallyrelevant negative phenotypes. That is, there was no detectable reductionin germination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 65 Analysis of ME19182 Events

ME19182 contains Ceres Annot:876419 (At4g01480, SEQ ID NO:1576) fromArabidopsis thaliana, which encodes a 216 amino acid inorganicpyrophosphatase protein. Evaluation of low-nitrogen tolerance forME19182 in T₂ and T₃ was conducted under the same conditions asdescribed in Examples 2 and 3. In this study, the seedlingphotosynthetic efficiency was measured as Fv/Fm comparing transgenicplants within an event to non-transgenic segregants pooled across thesame plate. Two events, -01 and -03, showed significantly increasedphotosynthetic efficiency on low ammonium nitrate-containing mediarelative to the internal controls in both generations at p≦0.05 using aone-tailed t-test assuming unequal variance. A summary of photosyntheticefficiency of ME19182 seedlings is shown in Table 71. ME19182 eventswere also tested for enhanced growth on the low ammonium nitrate media.No significant differences between the transgenics and the controls wereobserved.

TABLE 71 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 18 daysof growth on low ammonium nitrate. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME19182 ME19182-01 (T₂)0.64938 24 0.61988 154 2.47 × 10⁻² ME19182 ME19182-01 (T₃) 0.65546 130.61988 154 1.08 × 10⁻² ME19182 ME19182-03 (T₂) 0.64797 37 0.61988 1543.84 × 10⁻³ ME19182 ME19182-03 (T₃) 0.65388 26 0.61988 154 3.15 × 10⁻³

Events -01 and -03 segregated 2:1 and 3:1 respectively (R:S) for FINALE™resistance in the T2 generation.

Events -01 and -03 of ME19182 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 66 Analysis of ME20628 Events

ME20628 contains Ceres Annot:859276 (At2g21230, SEQ ID NO:175) fromArabidopsis thaliana, which encodes a 188 amino acid protein of unknownfunction. Evaluation of low-nitrogen tolerance for ME20628 in T₂ and T₃was conducted under the same conditions as described in Examples 2 and3. In this study, the seedling photosynthetic efficiency was measured asFv/Fm comparing transgenic plants within an event to non-transgenicsegregants pooled across the same plate. Two events, -03 and -04, showedsignificantly increased photosynthetic efficiency on lownitrate-containing media relative to the internal controls in bothgenerations at p≦0.05 using a one-tailed t-test assuming unequalvariance. A summary of photosynthetic efficiency of ME20628 seedlings isshown in Table 72. ME20628 events were also tested for enhanced growthon the low nitrate media as well as for increased photosyntheticefficiency and enhanced growth on low ammonium nitrate media. Nosignificant differences between the transgenics and the controls wereobserved.

TABLE 72 t-test comparison of seedling photosynthetic efficiency betweentransgenic seedlings and pooled non-transgenic segregants after 14 daysof growth on low nitrate media. Pooled Non-Trans- Transgenic genicst-test Line Events Fv/Fm n Fv/Fm n p-value ME20628 ME20628-03 (T₂)0.62771 42 0.58957  7 9.94 × 10⁻³ ME20628 ME20628-03 (T₃) 0.64375 200.61914 28 2.97 × 10⁻² ME20628 ME20628-04 (T₂) 0.62439 38 0.59667 124.78 × 10⁻² ME20628 ME20628-04 (T₃) 0.64768 22 0.61360 25 9.93 × 10⁻⁴

Events -03 and -04 segregated 3:1 (R:S) for FINALE™ resistance in the T₂generation.

Events -03 and -04 of ME20628 exhibited no statistically relevantnegative phenotypes. That is, there was no detectable reduction ingermination rate, the transgenic plants appeared wild type in allinstances; there was no observable or statistical differences betweentransgenics and controls in days to flowering; there was no observableor statistical differences between transgenics and controls in the sizeof the rosette area 7 days post-bolting; and there was no observable orstatistical differences between transgenics and controls in fertility(silique number and seed fill).

Example 67 Determination of Functional Homologs by Reciprocal BLAST

A candidate sequence was considered a functional homolog of a referencesequence if the candidate and reference sequences encoded proteinshaving a similar function and/or activity. A process known as ReciprocalBLAST (Rivera et al. (1998) Proc. Natl. Acad. Sci. USA, 95:6239-6244)was used to identify potential functional homolog sequences fromdatabases consisting of all available public and proprietary peptidesequences, including NR from NCBI and peptide translations from Ceresclones.

Before starting a Reciprocal BLAST process, a specific referencepolypeptide was searched against all peptides from its source speciesusing BLAST in order to identify polypeptides having BLAST sequenceidentity of 80% or greater to the reference polypeptide and an alignmentlength of 85% or greater along the shorter sequence in the alignment.The reference polypeptide and any of the aforementioned identifiedpolypeptides were designated as a cluster.

The BLASTP version 2.0 program from Washington University at SaintLouis, Mo., USA was used to determine BLAST sequence identity andE-value. The BLASTP version 2.0 program includes the followingparameters: 1) an E-value cutoff of 1.0e-5; 2) a word size of 5; and 3)the -postsw option. The BLAST sequence identity was calculated based onthe alignment of the first BLAST HSP (High-scoring Segment Pairs) of theidentified potential functional homolog sequence with a specificreference polypeptide. The number of identically matched residues in theBLAST HSP alignment was divided by the HSP length, and then multipliedby 100 to get the BLAST sequence identity. The HSP length typicallyincluded gaps in the alignment, but in some cases gaps were excluded.

The main Reciprocal BLAST process consists of two rounds of BLASTsearches; forward search and reverse search. In the forward search step,a reference polypeptide sequence, “polypeptide A,” from source speciesSA was BLASTed against all protein sequences from a species of interest.Top hits were determined using an E-value cutoff of 10⁻⁵ and a sequenceidentity cutoff of 35%. Among the top hits, the sequence having thelowest E-value was designated as the best hit, and considered apotential functional homolog or ortholog. Any other top hit that had asequence identity of 80% or greater to the best hit or to the originalreference polypeptide was considered a potential functional homolog orortholog as well. This process was repeated for all species of interest.

In the reverse search round, the top hits identified in the forwardsearch from all species were BLASTed against all protein sequences fromthe source species SA. A top hit from the forward search that returned apolypeptide from the aforementioned cluster as its best hit was alsoconsidered as a potential functional homolog.

Functional homologs were identified by manual inspection of potentialfunctional homolog sequences. Representative functional homologs for SEQID NO:3, SEQ ID NO:49, SEQ ID NO:77, SEQ ID NO:100, SEQ ID NO:152, SEQID NO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234,SEQ ID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ IDNO:510, SEQ ID NO:533, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769,SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:855, SEQ IDNO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ ID NO:982, SEQID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116, SEQ IDNO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ ID NO:1194, SEQ ID NO:1210,SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342, SEQ ID NO:1385, SEQ IDNO:1409, SEQ ID NO:1428, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510,SEQ ID NO:1525, SEQ ID NO:1537, SEQ ID NO:1554, SEQ ID NO:1577, and SEQID NO:1437 are shown in FIGS. 1-57, respectively. Additional exemplaryhomologs are correlated to certain Figures in the Sequence Listing.

Example 68 Determination of Functional Homologs by Hidden Markov Models

Hidden Markov Models (HMMs) were generated by the program HMMER 2.3.2.To generate each HMM, the default HMMER 2.3.2 program parameters,configured for global alignments, were used.

An HMM was generated using the sequences shown in FIG. 1 as input. Thesesequences were fitted to the model and a representative HMM bit scorefor each sequence is shown in the Sequence Listing. Additional sequenceswere fitted to the model, and representative HMM bit scores for any suchadditional sequences are shown in the Sequence Listing. The resultsindicate that these additional sequences are functional homologs of SEQID NO:3.

The procedure above was repeated and an HMM was generated for each groupof sequences shown in FIGS. 2-57, using the sequences shown in eachFigure as input for that HMM. A representative bit score for eachsequence is shown in the Sequence Listing. Additional sequences werefitted to certain HMMs, and representative HMM bit scores for suchadditional sequences are shown in the Sequence Listing. The resultsindicate that these additional sequences are functional homologs of thesequences used to generate that HMM.

VIII. OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method of producing a plant, said methodcomprising growing a plant cell comprising an exogenous nucleic acidmolecule, said exogenous nucleic acid molecule comprising a regulatoryregion operably linked to a nucleotide sequence encoding a polypeptide,wherein the HMM bit score of the amino acid sequence of said polypeptideis greater than about 20, said HMM based on the amino acid sequencesdepicted in one of FIGS. 1-57, and wherein said plant has a differencein the level of low-nitrogen tolerance as compared to the correspondinglevel of low-nitrogen tolerance of a control plant that does notcomprise said nucleic acid molecule.
 2. A method of producing a plant,said method comprising growing a plant cell comprising an exogenousnucleic acid molecule, said exogenous nucleic acid molecule comprising aregulatory region operably linked to a nucleotide sequence encoding apolypeptide having 80 percent or greater sequence identity to an aminoacid sequence selected from the group consisting of SEQ ID NO:3, SEQ IDNO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ IDNO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510,SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ IDNO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853,SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ IDNO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112,SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ IDNO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302,SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ IDNO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525,SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577, wherein a plantproduced from said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.
 3. The method of claim 1 or 2, wherein thepolypeptide comprises a Pfam domain having 70 percent or greatersequence identity to a Pfam domain in any one of the polypeptides in thesequence listing.
 4. A method of producing a plant, said methodcomprising growing a plant cell comprising an exogenous nucleic acidmolecule, said exogenous nucleic acid molecule comprising a regulatoryregion operably linked to a nucleotide sequence having 80 percent orgreater sequence identity to a nucleotide sequence selected from thegroup consisting of SEQ ID NO:1, SEQ ID NO:48, SEQ ID NO:76, SEQ IDNO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175, SEQ IDNO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ ID NO:245, SEQID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQ ID NO:532,SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612, SEQ IDNO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ ID NO:768, SEQID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQ ID NO:854,SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975, SEQ IDNO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ ID NO:1115,SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184, SEQ IDNO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ ID NO:1341,SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462, SEQ IDNO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ ID NO:1553,and SEQ ID NO:1576, or a fragment thereof, wherein a tissue of a plantproduced from said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.
 5. A method of producing a plant, said methodcomprising growing a plant cell comprising an exogenous nucleic acidmolecule, said exogenous nucleic acid molecule effective fordownregulating an endogenous nucleic acid molecule in the plant cell,wherein the endogenous nucleic acid molecule encodes a polypeptide, andwherein the HMM bit score of the amino acid sequence of the polypeptideis greater than about 20, said HMM based on the amino acid sequencesdepicted in one of FIGS. 1-57.
 6. A method of modulating the level oflow-nitrogen tolerance in a plant, said method comprising introducinginto a plant cell an exogenous nucleic acid molecule, said exogenousnucleic acid molecule comprising a regulatory region operably linked toa nucleotide sequence encoding a polypeptide, wherein the HMM bit scoreof the amino acid sequence of said polypeptide is greater than about 20,said HMM based on the amino acid sequences depicted in one of FIGS.1-57, and wherein a tissue of a plant produced from said plant cell hasa difference in the level of low-nitrogen tolerance as compared to thecorresponding level of low-nitrogen tolerance of a control plant thatdoes not comprise said exogenous nucleic acid molecule.
 7. A method ofmodulating the level of low-nitrogen tolerance in a plant, said methodcomprising introducing into a plant cell an exogenous nucleic acidmolecule, said exogenous nucleic acid molecule comprising a regulatoryregion operably linked to a nucleotide sequence encoding a polypeptidehaving 80 percent or greater sequence identity to an amino acid sequenceselected from the group consisting of SEQ ID NO:3, SEQ ID NO:49, SEQ IDNO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ IDNO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533,SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ IDNO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855,SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ IDNO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116,SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ IDNO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342,SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ IDNO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537,SEQ ID NO:1554, and SEQ ID NO:1577, wherein a tissue of a plant producedfrom said plant cell has a difference in the level of low-nitrogentolerance as compared to the corresponding level of low-nitrogentolerance of a control plant that does not comprise said nucleic acidmolecule.
 8. The method claim 1, wherein said polypeptide is selectedfrom the group consisting of SEQ ID NO:3, SEQ ID NO:49, SEQ ID NO:77,SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ ID NO:166, SEQ IDNO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQ ID NO:246, SEQID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510, SEQ ID NO:533,SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ ID NO:613, SEQ IDNO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQ ID NO:769, SEQID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853, SEQ ID NO:855,SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ ID NO:976, SEQ IDNO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112, SEQ ID NO:1116,SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ ID NO:1185, SEQ IDNO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302, SEQ ID NO:1342,SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ ID NO:1437, SEQ IDNO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525, SEQ ID NO:1537,SEQ ID NO:1554, and SEQ ID NO:1577.
 9. A method of modulating the levelof low-nitrogen tolerance in a plant, said method comprising introducinginto a plant cell an exogenous nucleic acid molecule, said exogenousnucleic acid molecule comprising a regulatory region operably linked toa nucleotide sequence having 80 percent or greater sequence identity toa nucleotide sequence selected from the group consisting of SEQ ID NO:1,SEQ ID NO:48, SEQ ID NO:76, SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151,SEQ ID NO:165, SEQ ID NO:175, SEQ ID NO:185, SEQ ID NO:207, SEQ IDNO:217, SEQ ID NO:233, SEQ ID NO:245, SEQ ID NO:299, SEQ ID NO:331, SEQID NO:367, SEQ ID NO:509, SEQ ID NO:532, SEQ ID NO:555, SEQ ID NO:557,SEQ ID NO:592, SEQ ID NO:612, SEQ ID NO:645, SEQ ID NO:686, SEQ IDNO:729, SEQ ID NO:745, SEQ ID NO:768, SEQ ID NO:791, SEQ ID NO:823, SEQID NO:827, SEQ ID NO:852, SEQ ID NO:854, SEQ ID NO:890, SEQ ID NO:916,SEQ ID NO:943, SEQ ID NO:975, SEQ ID NO:981, SEQ ID NO:1053, SEQ IDNO:1098, SEQ ID NO:1111, SEQ ID NO:1115, SEQ ID NO:1156, SEQ ID NO:1158,SEQ ID NO:1165, SEQ ID NO:1184, SEQ ID NO:1193, SEQ ID NO:1209, SEQ IDNO:1273, SEQ ID NO:1301, SEQ ID NO:1341, SEQ ID NO:1384, SEQ ID NO:1408,SEQ ID NO:1427, SEQ ID NO:1462, SEQ ID NO:1490, SEQ ID NO:1509, SEQ IDNO:1524, SEQ ID NO:1536, SEQ ID NO:1553, and SEQ ID NO:1576, or afragment thereof, wherein a tissue of a plant produced from said plantcell has a difference in the level of low-nitrogen tolerance as comparedto the corresponding level of low-nitrogen tolerance of a control plantthat does not comprise said nucleic acid molecule.
 10. A plant cellcomprising an exogenous nucleic acid molecule, said exogenous nucleicacid molecule comprising a regulatory region operably linked to anucleotide sequence encoding a polypeptide, wherein the HMM bit score ofthe amino acid sequence of said polypeptide is greater than about 20,said HMM based on the amino acid sequences depicted in one of FIGS.1-57, and wherein said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.
 11. A plant cell comprising an exogenous nucleicacid molecule said exogenous nucleic acid molecule comprising aregulatory region operably linked to a nucleotide sequence encoding apolypeptide having 80 percent or greater sequence identity to an aminoacid sequence selected from the group consisting of SEQ ID NO:3, SEQ IDNO:49, SEQ ID NO:77, SEQ ID NO:97, SEQ ID NO:100, SEQ ID NO:152, SEQ IDNO:166, SEQ ID NO:186, SEQ ID NO:208, SEQ ID NO:218, SEQ ID NO:234, SEQID NO:246, SEQ ID NO:300, SEQ ID NO:332, SEQ ID NO:368, SEQ ID NO:510,SEQ ID NO:533, SEQ ID NO:556, SEQ ID NO:558, SEQ ID NO:593, SEQ IDNO:613, SEQ ID NO:646, SEQ ID NO:687, SEQ ID NO:730, SEQ ID NO:746, SEQID NO:769, SEQ ID NO:792, SEQ ID NO:824, SEQ ID NO:828, SEQ ID NO:853,SEQ ID NO:855, SEQ ID NO:891, SEQ ID NO:917, SEQ ID NO:944, SEQ IDNO:976, SEQ ID NO:982, SEQ ID NO:1054, SEQ ID NO:1099, SEQ ID NO:1112,SEQ ID NO:1116, SEQ ID NO:1157, SEQ ID NO:1159, SEQ ID NO:1166, SEQ IDNO:1185, SEQ ID NO:1194, SEQ ID NO:1210, SEQ ID NO:1274, SEQ ID NO:1302,SEQ ID NO:1342, SEQ ID NO:1385, SEQ ID NO:1409, SEQ ID NO:1428, SEQ IDNO:1437, SEQ ID NO:1463, SEQ ID NO:1491, SEQ ID NO:1510, SEQ ID NO:1525,SEQ ID NO:1537, SEQ ID NO:1554, and SEQ ID NO:1577, wherein a tissue ofa plant produced from said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.
 12. A plant cell comprising an exogenous nucleicacid molecule said exogenous nucleic acid molecule comprising aregulatory region operably linked to a nucleotide sequence having 80percent or greater sequence identity to a nucleotide sequence selectedfrom the group consisting of SEQ ID NO:1, SEQ ID NO:48, SEQ ID NO:76,SEQ ID NO:96, SEQ ID NO:99, SEQ ID NO:151, SEQ ID NO:165, SEQ ID NO:175,SEQ ID NO:185, SEQ ID NO:207, SEQ ID NO:217, SEQ ID NO:233, SEQ IDNO:245, SEQ ID NO:299, SEQ ID NO:331, SEQ ID NO:367, SEQ ID NO:509, SEQID NO:532, SEQ ID NO:555, SEQ ID NO:557, SEQ ID NO:592, SEQ ID NO:612,SEQ ID NO:645, SEQ ID NO:686, SEQ ID NO:729, SEQ ID NO:745, SEQ IDNO:768, SEQ ID NO:791, SEQ ID NO:823, SEQ ID NO:827, SEQ ID NO:852, SEQID NO:854, SEQ ID NO:890, SEQ ID NO:916, SEQ ID NO:943, SEQ ID NO:975,SEQ ID NO:981, SEQ ID NO:1053, SEQ ID NO:1098, SEQ ID NO:1111, SEQ IDNO:1115, SEQ ID NO:1156, SEQ ID NO:1158, SEQ ID NO:1165, SEQ ID NO:1184,SEQ ID NO:1193, SEQ ID NO:1209, SEQ ID NO:1273, SEQ ID NO:1301, SEQ IDNO:1341, SEQ ID NO:1384, SEQ ID NO:1408, SEQ ID NO:1427, SEQ ID NO:1462,SEQ ID NO:1490, SEQ ID NO:1509, SEQ ID NO:1524, SEQ ID NO:1536, SEQ IDNO:1553, and SEQ ID NO:1576, or a fragment thereof, wherein a tissue ofa plant produced from said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.
 13. A transgenic plant comprising the plant cellof claim 10 or
 11. 14. The transgenic plant of claim 13, wherein saidplant is a member of a species selected from the group consisting ofPanicum virgatum (switchgrass), Sorghum bicolor (sorghum, sudangrass),Miscanthus giganteus (miscanthus), Saccharum sp. (energycane), Populusbalsamifera (poplar), Zea mays (corn), Glycine max (soybean), Brassicanapus (canola), Triticum aestivum (wheat), Gossypium hirsutum (cotton),Oryza sativa (rice), Helianthus annuus (sunflower), Medicago sativa(alfalfa), Beta vulgaris (sugarbeet), or Pennisetum glaucum (pearlmillet).
 15. A transgenic plant of claim 13, wherein said polypeptide isany one of the polypeptides in the sequence listing.
 16. A productcomprising plant tissue from a transgenic plant according to claim 14.17. An isolated nucleic acid molecule comprising a nucleotide sequencehaving 95% or greater sequence identity to the nucleotide sequence setforth in SEQ ID NOs: 5, 7, 37, 50, 52, 54, 66, 79, 86, 91, 103, 105,107, 109, 112, 114, 124, 127, 136, 140, 143, 153, 155, 157, 159, 161,163, 167, 169, 171, 175, 176, 178, 187, 189, 202, 215, 219, 221, 226,228, 235, 237, 240, 247, 250, 252, 258, 261, 269, 273, 280, 301, 303,305, 307, 311, 313, 315, 317, 330, 331, 333, 379, 387, 389, 397, 429,431, 442, 457, 462, 466, 470, 472, 480, 486, 512, 514, 516, 518, 520,522, 524, 526, 528, 534, 537, 540, 551, 557, 568, 570, 574, 582, 587,594, 596, 598, 600, 602, 604, 606, 608, 614, 616, 621, 623, 625, 627,629, 631, 633, 635, 637, 639, 641, 647, 649, 651, 653, 655, 657, 659,661, 663, 665, 667, 669, 673, 677, 688, 690, 692, 698, 700, 702, 704,709, 711, 713, 715, 717, 719, 731, 734, 736, 739, 743, 747, 749, 756,759, 780, 795, 797, 811, 829, 831, 835, 841, 843, 852, 854, 857, 859,861, 863, 867, 869, 871, 875, 879, 881, 883, 890, 892, 897, 899, 918,922, 924, 930, 934, 936, 938, 941, 945, 949, 951, 955, 959, 961, 963,965, 975, 979, 981, 983, 994, 1002, 1006, 1010, 1014, 1017, 1020, 1022,1024, 1038, 1042, 1056, 1060, 1062, 1064, 1066, 1073, 1079, 1100, 1107,1117, 1119, 1121, 1127, 1130, 1137, 1160, 1165, 1168, 1170, 1172, 1176,1178, 1181, 1186, 1195, 1197, 1199, 1201, 1212, 1214, 1217, 1227, 1231,1250, 1252, 1254, 1256, 1258, 1260, 1262, 1275, 1277, 1279, 1283, 1286,1288, 1290, 1292, 1304, 1306, 1308, 1310, 1332, 1343, 1353, 1386, 1388,1408, 1410, 1412, 1414, 1416, 1420, 1422, 1427, 1429, 1431, 1433, 1435,1438, 1441, 1443, 1449, 1451, 1462, 1464, 1466, 1468, 1470, 1472, 1478,1489, 1490, 1492, 1494, 1498, 1500, 1509, 1511, 1513, 1519, 1524, 1526,1528, 1536, 1538, 1542, 1544, 1546, 1549, 1553, 1556, 1558, 1560, 1562,1564, 1568, 1570, 1576, 1579, 1581, 1583, 1585, 1587, 1593, 1600, 1606,1610, 1614, 1620, 1630, 1632, 1640, 1642, 1644, 1646,
 1654. 18. Anisolated nucleic acid molecule comprising a nucleotide sequence encodinga polypeptide having 80% or greater sequence identity to the amino acidsequence set forth in SEQ ID NOs: 6, 8, 38, 51, 53, 55, 67, 80, 87, 92,100, 104, 106, 108, 110, 113, 115, 125, 128, 137, 141, 144, 154, 156,158, 160, 162, 164, 168, 170, 172, 177, 179, 188, 190, 203, 216, 220,222, 227, 229, 236, 238, 241, 248, 251, 253, 259, 262, 270, 274, 279,281, 302, 304, 306, 308, 312, 314, 316, 318, 332, 334, 338, 368, 380,384, 388, 390, 398, 430, 432, 443, 458, 463, 467, 471, 473, 481, 487,513, 515, 517, 521, 523, 525, 527, 529, 535, 538, 541, 552, 558, 569,571, 575, 583, 588, 595, 597, 599, 601, 603, 605, 607, 609, 615, 617,622, 624, 626, 628, 630, 632, 634, 636, 638, 640, 642, 648, 650, 652,654, 656, 658, 660, 662, 664, 666, 668, 670, 674, 678, 687, 689, 691,693, 699, 701, 703, 705, 710, 712, 714, 716, 718, 720, 732, 735, 737,740, 744, 748, 750, 760, 769, 781, 796, 798, 812, 830, 832, 836, 842,844, 853, 855, 858, 860, 862, 864, 868, 870, 876, 880, 882, 884, 891,893, 898, 900, 919, 923, 925, 931, 935, 937, 939, 942, 946, 950, 952,956, 960, 962, 964, 966, 976, 980, 982, 984, 995, 1003, 1007, 1011,1015, 1018, 1021, 1023, 1025, 1039, 1043, 1057, 1061, 1063, 1065, 1067,1074, 1080, 1099, 1101, 1108, 1116, 1118, 1120, 1122, 1128, 1131, 1138,1161, 1166, 1169, 1171, 1173, 1175, 1177, 1179, 1182, 1187, 1196, 1198,1200, 1202, 1203, 1213, 1215, 1218, 1228, 1232, 1251, 1253, 1255, 1257,1259, 1261, 1263, 1276, 1278, 1280, 1287, 1289, 1291, 1293, 1305, 1307,1309, 1311, 1333, 1344, 1354, 1366, 1387, 1389, 1409, 1411, 1413, 1415,1417, 1421, 1428, 1430, 1432, 1434, 1436, 1437, 1439, 1442, 1450, 1452,1463, 1465, 1467, 1469, 1471, 1473, 1479, 1480, 1486, 1491, 1493, 1495,1499, 1501, 1510, 1512, 1514, 1520, 1525, 1527, 1529, 1537, 1539, 1543,1545, 1547, 1550, 1554, 1557, 1559, 1561, 1563, 1565, 1569, 1571, 1577,1580, 1582, 1584, 1586, 1588, 1594, 1601, 1607, 1611, 1615, 1621, 1627,1631, 1633, 1635, 1643,
 1645. 19. A method of identifying whether apolymorphism is associated with variation in a trait, said methodcomprising: a) determining whether one or more genetic polymorphisms ina population of plants is associated with the locus for a polypeptideselected from the group consisting of the polypeptides depicted in FIGS.1-57, SEQ ID NO:556, SEQ ID NO:853, and SEQ ID NO:1157 and functionalhomologs thereof; and b) measuring the correlation between variation insaid trait in plants of said population and the presence of said one ormore genetic polymorphisms in plants of said population, therebyidentifying whether or not said one or more genetic polymorphisms areassociated with variation in said trait.
 20. A method of identifyingwhether a polymorphism is associated with variation in a trait, saidmethod comprising: a) screening a population of plants to determinewhether one or more genetic polymorphisms in said population of plantsis associated with the locus for a polypeptide selected from the groupconsisting of the polypeptides depicted in FIGS. 1-57; SEQ ID NO: 556,SEQ ID NO: 853, and SEQ ID NO: 1157 and functional homologs thereof; b)measuring the correlation between variation in said trait in plants ofsaid population and the presence of said one or more geneticpolymorphisms in plants of said population, thereby identifying whetheror not said one or more genetic polymorphisms are associated withvariation in said trait; c) selecting from said population of plants asub-population of plants that possess said one or more geneticpolymorphisms associated with said trait; and d) crossing one or moreplants from said sub-population of plants.
 21. The method according toclaim 20, further comprising breeding said sub-population of plants toproduce a plant line which comprises said polymorphism.
 22. A method ofmaking a plant line, said method comprising: a) determining whether oneor more genetic polymorphisms in a population of plants is associatedwith the locus for a polypeptide selected from the group consisting ofthe polypeptides depicted in FIGS. 1-57, SEQ ID NO:556, SEQ ID NO:853,and SEQ ID NO:1157 and functional homologs thereof; b) identifying oneor more plants in said population in which the presence of at least oneallele at said one or more genetic polymorphisms is associated withvariation in a trait; c) crossing each said one or more identifiedplants with itself or a different plant to produce seed; d) crossing atleast one progeny plant grown from said seed with itself or a differentplant; and e) repeating steps c) and d) for an additional 0-5generations to make said plant line, wherein said at least one allele ispresent in said plant line.
 23. The method of claim 19 or 20, whereinsaid trait is the level of low-nitrogen tolerance.
 24. The method ofclaim 19 or 20, wherein said population is a population of switchgrass,sorghum, sugar cane, or miscanthus plants.
 25. A plant cell comprisingan exogenous nucleic acid molecule, said exogenous nucleic acid moleculecomprising a regulatory region operably linked to a nucleic acidmolecule encoding a polypeptide having 80 percent or greater sequenceidentity to an amino acid sequence selected from the sequence listing,wherein a tissue of a plant produced from said plant cell has adifference in the level of low-nitrogen tolerance as compared to thecorresponding level of low-nitrogen tolerance of a control plant thatdoes not comprise said nucleic acid molecule.
 26. A plant cellcomprising an exogenous nucleic acid molecule, said exogenous nucleicacid comprising a regulatory region operably linked to a nucleic acidmolecule having 80 percent or greater sequence identity to a nucleotidesequence selected from the sequence listing, wherein a tissue of a plantproduced from said plant cell has a difference in the level oflow-nitrogen tolerance as compared to the corresponding level oflow-nitrogen tolerance of a control plant that does not comprise saidnucleic acid molecule.